Scientific Publications 2004
2004. "Accumulation of Mn(II) in Deinococcus radiodurans Facilitates Gamma-Radiation Resistance." Science 306(5698):1025-1028. Abstract Deinococcus radiodurans is extremely resistant to ionizing radiation. How this bacterium can grow under chronic -radiation (50 Gy/hour) or recover from acute doses greater than 10 kGy is unknown. We show that D. radiodurans accumulates very high intracellular manganese and low iron levels compared to radiation sensitive bacteria, and resistance exhibits a concentration-dependent response to Mn(II). Among the most radiation-resistant bacterial groups reported, Deinococcus, Enterococcus, Lactobacillus and cyanobacteria spp. accumulate Mn(II). In contrast, Shewanella oneidensis and Pseudomonas putida have high Fe but low intracellular Mn concentrations and are very sensitive. We propose that Mn(II) accumulation facilitates recovery from radiation injury.
2004. "Adsorption, Desorption, and Clustering H20 on Pt (111)." Journal of Chemical Physics 120(3):1516-1523. Abstract The adsorption, desorption, and clustering behavior of H20 on Pt(111) has been investigated by specular He scattering. The data show that water adsorbed on a clean Pt(111) surface undergoes a transition from a random to a clustered structure near 60 K. The initial helium scattering cross sections as a function of temperature are found to be insensitive to H20 flux over a range of 0.005 ML/s to 0.55 ML/s indicating the clustering process is more complex than simple surface diffusion. The coarsening process of an initially random distribution of water deposited at 25 K is found to occur over a broad temperature range, 60 K< T <140 K, during thermal annealing. The desorption kinetics for submonolayer water are determined to be zero-order for surface coverages greater than 0.05 ML and temperatures between 150 K and 174 K. The zero-order desorption kinetics are consistent with a two-dimensional two-phase coexistence between H2O condensed phase and a 2-gas phase on the Pt surface
2004. "Reduced Spectral Density Mapping of a Partially Folded Fragment of E. Coli Thioredoxin. ." Journal of Biomolecular Structure and Dynamics 21(5):663-670. Abstract The backbone dynamics of a partially folded, N-terminal fragment of E. coli thioredoxin were investigated using nuclear magnetic resonance spectroscopy (NMR). Relaxation data were collected at three temperatures and analyzed using reduced spectral density mapping. As temperature was increased, the values for the viscosity normalized J(0) and for J(omegaH) increased, while J(omegaN) decreased. The global trend observed for the viscosity normalized J(0) was consistent with an increase in the hydrodynamic volume of the fragment and suggested the presence of correlated rotational motion in the absence of long range interactions. In addition, the residue specific variation observed for the viscosity normalized J(0) suggested contributions to J(omega) from a range of correlation times that are close to the global correlation time.
2004. "X-ray Photoelectron Spectroscopic Analyses of Corrosion Products Formed on Rock Bolt Carbon Steel in Chloride Media with Bicarbonate and Silicate Ions." Corrosion Science 46(11):2629-2649. Abstract The passivation behavior of Yucca Mountain Repository rock bolt carbon steel in deaerated 3.5% NaCl solution containing SiO₂_₃ and HCO_₃ ions was investigated by potentiodynamic polarization, electrochemical impedance spectroscopy, scanning electron microscopy, and X-ray photoelectron spectroscopic methods. Polarization results indicate that combinations of silicate and bicarbonate anions decrease the passive current density and raise the pitting potential. XPS results indicate the enrichment of silica at passive potentials and the formation of mixed FeCO₃ and silica film at lower potentials. This change in film composition was responsible for the changes in corrosion rate at lower and higher potentials. XPS results also support the thermodynamic data with regard to the occurrence of second oxidation peak observed in the polarization curves to be due to the oxidation of FeCO₃ to Fe2O₃
2004. "Amorphization of Silicon Carbide by Carbon Displacement." Applied Physics Letters 84(19):3909-3911. Abstract We have used molecular dynamics simulations to examine the possibility of amorphizing silicon carbide (SiC) by exclusively displacing C atoms. At a defect generation corresponding to 0.2 displacements per atom, the enthalpy surpasses the level of melt-quenched SiC, the density decreases by about 15%, and the radial distribution function shows a lack of long-range order. Prior to amorphization, the surviving defects are mainly C Frenkel pairs (67%), but Si Frenkel pairs (18%) and anti-site defects (15%) are also present. The results indicate that SiC can be amorphized by C sublattice displacements. Chemical short-range disorder, arising mainly from interstitial production, plays a significant role in the amorphization.
2004. "Molecular Dynamics Simulation of Disordered Zircon." Physical Review. B, Condensed Matter and Materials Physics 69(6):064115, 1-9. Abstract The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.
2004. "A Multispectrum Analysis of the 2v2 Spectral Region of H12C14N: Intensities, Broadening and Pressure-Shift Coefficients." Journal of Quantitative Spectroscopy and Radiative Transfer 87(3-4):339-366. Abstract High-resolution (0.005 cm-1) infrared absorption spectra of HCN in the 2v2 band region near 1411 cm-1 have been recorded at room temperature using the Bruker IFS120HR Fourier transform spectrometer located at Pacific Northwest National Laboratory. Four spectra of high-purity (99.8%) HCN together with three spectra of lean mixtures (~3%) of HCN in dry air were simultaneously fit using a multispectrum non-linear least-squares procedure. The analysis yielded room temperature values for absolute intensities, self- and air-broadening coefficients, and self- and air-broadening coefficients for numerous lines in the 2v2 band of H13C14N, were also determined. Since there are no previous measurements of broadening and shift parameters reported in the 2v2 band, our results are compared with values recently determined in the v1 band of H13C14N and with current HITRAN values.
2004. "Low-Lying Electronic States of FeNC and FeCN: A Theoretical Journey into Isomerization and Quartet/Sextet Competition ." Journal of Chemical Physics 120(10):4726-4741. Abstract The abstract for this product is not available at this time.
2004. "Improving Modeling of Iodine-129 Groundwater Contamination Plumes Using the System Assessment Capability." Journal of Undergraduate Research IV:53-59. Abstract Years of production of radioactive materials at the Hanford Site in southeastern Washington State has resulted in contamination of surface, subsurface, and surface water environments. Cleanup of the site has been aided by various tools, including computer software used to predict contaminant migration in the future and estimate subsequent impacts. The System Assessment Capability (SAC) is a total systems tool designed to simulate the movement of contaminants from all waste sites at Hanford through the vadose zone, the unconfined aquifer, and the Columbia River. Except for iodine-129, most of the contaminants modeled by SAC have acceptably matched field measurements. The two most likely reasons for the inconsistency between the measured field data and SAC modeled predictions are an underestimated inventory and an overestimated sorption value (Kd). Field data tend to be point measurements taken from near the surface of the unconfined aquifer. Thus, the depth of the iodine-129 contamination plume on the site is not well characterized. Geostatistical analyses of the measured data were conducted to determine the mass of iodine-129 for four assumed plume depths within the unconfined aquifer. Several simulations for two different Kd’s using the initial SAC inventory were run to determine the effect of an overestimated sorption value on SAC modeled predictions. The initial SAC inventory was then increased for the two different Kd’s to determine the influence of an underestimated inventory on SAC modeled predictions. It was found that evidence for both an underestimated inventory and for an overestimated sorption value for iodine-129 exist. These results suggest that the Kd for iodine-129 should be reevaluated and that a more complete inventory must be generated in order to more accurately model iodine-129 groundwater contamination plumes that match available field data.
2004. "A Comparison Between Conventional and Ultrasound-Mediated Heterogeneous Catalysis: Hydrogenation of 3-buten-1-ol Aqueous Solutions." Journal of Catalysis 221(2):347-353. Abstract A power flow scheme applicable to probe-type ultrasound reactors is presented, that has been deduced from both experimental measurements employing an unjacketed vessel and theoretical predictions. Under typical conditions for water, 77% of the electrical power is converted into mechanical motion of the probe, that in turn is dissipated to both acoustic power (~12%) and cavitational heating (~88%). Approximately 92% of the mechanical power of the probe was converted into heat, with the remaining power presumably converted into audible acoustic and/or mechanical motion. Heterogeneous catalysis experiments have been performed at 298 K in an isothermal (i.e., jacketed) reaction vessel comparing chemistry in conventional (e.g., thermal) versus ultrasound-assisted systems. Both product state distribution and reaction rate measurements have been performed for the hydrogenation (using hydrogen gas) of aqueous 3-buten-1-ol solutions employing Pd-black powder. Products from the heterogeneous catalysis include isomerization to cis and trans 2-buten-1-ol, as well as hydrogenation to 1-butanol. Based on the observed differences in cis- to trans- 2-buten-1-ol ratios in conventional experiments, employing untreated and pre-reduced catalysts, it has been determined that a kinetic effect controls the observed product state distribution. In addition, differences in the ratio between cis- plus trans- 2-buten-1-ol to 1-butanol, comparing ultrasound-assisted to conventional catalysis, reveal a ~5-fold enhancement in isomerization relative to the more energetically favored hydrogenation due to application of ultrasound. Finally, the product formation rates for 1-butanol, as well as isomerization plus hydrogenation, revealed that conventional and ultrasound experiments showed both a non-linear dependence with applied ultrasound power and no differences between untreated and pre-reduced catalysts. The observed reaction rate enhancements were 1:36:183 for the conventional, 90 W ultrasound, and 190 W ultrasound experiments, respectively.
2004. "The Effect of Cavitating Ultrasound on the Heterogeneous AqueousHydrogenation of 3-buten-2-ol on Pd-black." Journal of Catalysis 227(2):552-555. Abstract The effect of ultrasound at 20 kHz on the heterogeneous aqueous hydrogenation of 3-buten-2-ol employing a Pd-black catalyst has been studied isothermally at 295 K, forming 2-butanone and 2-butanol products. Our work here shows that adding 1-pentanol as an inert dopant had the effect of inducing cavitation in the ultrasound-treated reaction where it otherwise would not occur. The selectivity showed a 700% increase toward 2-butanol formation and the activity enhanced a factor of 10.8 compared to the noncavitating high-power ultrasound experiment. This study demonstrates that “inert dopants” may have use as synthetic tools in sonocatalysis.
2004. "Enthalpies of Formation of Gas-Phase N3, N3-, N5+, and N5- from Ab Initio Molecular Orbital Theory, Stability Predictions for N5+N3- and N5+N5-, and Experimental Evidence for the Instability of N5+N3-." Journal of the American Chemical Society 126(3):834-843. doi:10.1021/ja0303182 Abstract Ab initio molecular orbital theory has been used to calculate accurate enthalpies of formation and adiaatic electron affinities or ionization potentials for N3, N3-, N5+, and N5- from total atomization energies. Born-Haber cycle calculations, using estimated lattice energies and the adiabatic ionization potentials of the anions and electron affinities of the cations, permit for the first time reliable stability predictions for the hypthetical N5+N3- and N5+N5- salts. Contrary to previous predictions, it is shown that neither salt can be stabilized, decomposing spontaneously to N3 radicals and N2. This conclusion was experimentally confirmed by low-temperature metathetical reactions between N5SbF6 and alkali metal azides in different solvents, resulting in violent reactions with spontaneous nitrogen evolution. It is also shown that the vertical ionization potentials and electron affinities, used in previous stability predictions, must not be used in stability predictions involving species, such as N5 ions, because the resulting N5 radicals are not vibrationally stable and undergo spontaneous further decomposition. The use of the vertical values, that neglects this highly exothermic secondary decompositon of N5 to N3 and N2, results in large errors of about 100 kcal/mol for each N5 unit.
2004. "Zeolite Nanoclusters Coated onto the Mesopore Walls of SBA-15." Journal of the American Chemical Society 126(44):14324-14325. Abstract Hydrothermal stability and acidity are both essential for the application of mesoporous materials in catalysis.1,2 Several approaches have been aimed at improving these roperties;3-8 for example, hydrothermally stable and strongly acidic mesoporous aluminosilicates have been assembled using protozeolitic seeds.
2004. "Electron Microscopy Evaluation of the Role of Dissimilatory Metal-reducing Bacteria in Biomineralization Pathways." Microscopy and Microanalysis 10(suppl 2):1538-1539. Abstract The importance of microorganisms in the biogeochemical cycling of Fe is well-recognized . Dissimilatory metal-reducing bacteria (DMRB), which are ubiquitous in soils and aquifers, couple the oxidation of organic matter or H2 with the reduction of various Fe(III) oxide phases to obtain energy for growth and function. They can also catalyze Fe(III) reduction under anaerobic conditions, utilizing crystalline and poorly crystalline iron oxides as a terminal electron acceptor. Microbially induced Fe mineral transformations were examined using the Shewanella putrefaciens, strain CN32 in an artificial groundwater medium in columns under advective flow conditions. Columns were filled with ferrihydrite-coated quartz sand inoculated with S. putrefaciens (initial cell density 10⁸ mL-¹). Lactate was added as an electron donor. Changes in microbial metabolism, aqueous chemistry, and solid phase distributions were monitored at time points until termination of the column experiment at 16 days . Transmission (TEM) and scanning electron microscopy (SEM) was used for investigating mineral association with bacterial cells, crystal size, morphology, and spatial relationships. A special TEM sample preparation protocol developed in our laboratory was used for the accurate preservation of both the biological and mineral portion of the sample . To eliminate the anaerobic sample exposure to oxygen, the whole embedding procedure, as well as the thin sectioning on an ultramicrotome was carried out in an anaerobic glove box (95% argon, 5% hydrogen). Ultra thin sections of the material were studied using a JEOL 2010 TEM operating at 200 kV coupled to an Oxford EDS system. Images were collected and analyzed using a Digital Micrograph (Gatan). Selected area diffraction patterns were evaluated by the Desktop Microscopist (Lacuna) software. Visual changes in the solid-phase within the column were evident: initial orange ferrihydrite started turning brown, and further darkened over the course of the experiment, as it was converted to predominantly goethite and magnetite [Fig. 1A, 1B]. In addition to spectroscopic methods, the presence of goethite and magnetite was further confirmed by TEM and SEM, and the spatial orientations and particle size of mineral particles were determined. Typical needle-like structures of goethite crystals were predominantly associated with the surface of ferrihydrite, but were also found coupled with microbial cell surfaces. In fact, some bacterial cells appeared completely encrusted in goethite, most likely, a result of electrostatic attraction between newly precipitated goethite and the microbial surface. Magnetite, on the other hand, was mainly associated with the ferrihydrite surface, and only rarely with the cell surface. Thus, the bacterial cell is only indirectly (by ferrous iron production) responsible for goethite and magnetite formation. Although intracellular precipitation of iron oxides in S. putrefaciens was recently reported , only extracellular precipitation was observed in this experimental setup. The ability of bacteria to shed the mineral deposits from their outer membranes in order to prevent their surfaces passivation caused by mineral sorption will be discussed. Bacteria appeared to primarily serve as an Fe(II) source for the system; secondary mineralization was confirmed as a function of initial Fe(II) concentrations. The mechanism of the enzymatic reduction is not completely understood, and the accountable protein functions are being intensively investigated by several molecular biology techniques. Current and future studies will include immunogold labeling at the electron microscopy level as a method for determining the localization of these proteins.
2004. "Interactions of Gaseous Nitric Acid with Surfaces of Environmental Interest." Physical Chemistry Chemical Physics. PCCP 6(14):3879-3888. Abstract Gaseous nitric acid removal by surfaces in experimental systems and in the atmospheric boundary layer is rapid. However, neither the form of HNO₃ on surfaces nor its impact on the properties of the thin surface film are known. We report here studies of surfaces that have been exposed at room temperature (295 ± 2 K) to gaseous mixtures of water vapor with HNO₃ at concentrations from 46 ppb to 4 x 10³ ppm. The surfaces were probed using a combination of Fourier transform infrared spectrometry (FTIR), non-contact atomic force microscopy (AFM), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and X-ray photoelectron spectroscopy (XPS). Exposure of borosilicate glass, quartz, and thin Teflon films to mixtures of gaseous HNO₃ and water vapor leads to the subsequent uptake of much larger amounts of water than occurs on the corresponding unexposed surfaces. Infrared spectra show evidence for the formation of nitric acid–water complexes on the surface that leads to this enhanced water uptake. On borosilicate glass, exposure to the nitric acid–water vapor mixture results in surface segregation of the trace metal oxides and their nitrates formed from reaction with HNO₃. The majority of these oxides can be removed by rinsing with water; however, smaller, segregated regions of ZnO remain on the surface. The implications for heterogeneous reactions in thin films on surfaces in laboratory systems and in the atmosphere are discussed.
2004. "A QM/MM Study of Aqueous Solvation of the Uranyl Fluoride [UO₂F₄₂] complex." Theoretical Chemistry Accounts 112:403-409. Abstract The abstract for this product is not available at this time.
2004. "Relativistic Double-Zeta, Triple-Zeta, and Quadruple-Zeta Basis Sets for the 5d Elements Hf-Hg." Theoretical Chemistry Accounts 112:403-409. doi:10.1007/s00214-004-0607-y Abstract No abstract for this article is available at this time.