Geochemistry/Biogeochemistry/Subsurface Publications

2009

Bose S, MF Hochella, YA Gorby, DW Kennedy, DE Mccready, AS Madden, and BH Lower. 2009. "Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 73(4):962-976. Abstract The surface area normalized reduction rates of hematite (α-Fe2O3) nanoparticles, ranging in size from 11 to 99 nm, by S. oneidensis MR-1 with lactate as the sole electron donor were measured. The reduction kinetics of metal-oxide nanoparticles were examined to determine how S. oneidensis utilizes these environmentally-relevant solid-phase electron acceptors. Nanoparticles involved in geochemical reactions show different properties relative to larger particles of the same phase, and their reactivity is predicted to change as a function of size. As evident from whole cell TEM mounts, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11, 12, and 99 nm nanoparticles and the less aggregated 30 and 43 nm rhombohedral particles. Due to the aggregation differences, the 11, 12 and 99 nm particles show less cell contact and coverage than the 30 and 43 nm particles, but the former still show significant rates of reduction. This leads to the provisional speculation that S. oneidensis MR-1 employs a pathway of indirect electron transfer in conjunction with the direct-contact pathway, and the relative importance of the bioreduction mechanism employed may depend upon aggregation level, shape of the particles, and/or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles with reduction in size, the smallest particles (11 nm) exhibit a one order of magnitude decrease in reduction rate (surface area normalized) when compared with larger (99 nm) nanoparticles, and the 12 nm rate falls in between these two. This effect may also be due to the passivation of the mineral and cell surfaces by Fe(II), or decreasing solubility due to decrease in size.
Wigginton NS, KM Rosso, AG Stack, and MF Hochella. 2009. "Long-Range Electron Transfer Across Cytochrome-Hematite (a-Fe2O3) Interfaces." Journal of Physical Chemistry C 113(6):2096-2103. Abstract Electrochemical scanning tunneling microscopy (EC-STM) was used to assess the distance dependence of electron tunneling facilitated by a bacterial multiheme cytochrome to a single crystal iron oxide surface. We measured tunneling current-distance (I-s) profiles across the nanoscale space between insulated Au STM tips and the basal (001) surface of a hematite (-Fe2O3) crystal, and compared them to the case in which an intervening small tetraheme cytochrome (STC) from Shewanella oneidensis covalently linked to the Au tip surface. Tunneling profiles were collected at constant surface potentials in solutions having a range of ionic strengths. At short tip-sample separation, the distance dependece of the tunneling current shows a quasi-linear behavior. At longer distances it shows an exponential decay. The different regions are discussed in terms of ordering of interfacial water and ion layers in the electrical double layer associated with the hematite surface. The effective tunneling range and its rate of decay are substantially increased when STC is present in the tunneling junction, suggesting that cytochrome molecules provide enhanced tunneling pathways and stronger electronic coupling to the hematite surface. Based on these results, cytochrome-mediated electron transfer during bacterial metal reduction may be possible at distances further than originally thought. Also, as multiheme cytochromes and other similar molecules gain attention for their promising role in fuel cells and molecular electronics, we show that the solution conditions and surface properties of the substrate must be carefully considered.
Lower BH, R Yongsunthon, L Shi, L Wildling, HJ Gruber, NS Wigginton, CL Reardon, GE Pinchuk, T Droubay, JF Boily, and SK Lower. 2009. "Antibody recognition force microscopy shows that outer membrane cytochromes OmcA and MtrC are expressed on the exterior surface of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 75(9):2931-2935. Abstract Antibody-recognition force microscopy showed that OmcA and MtrC are expressed on the exterior surface of living Shewanella oneidensis MR-1 cells during anaerobic growth, when Fe(III) served as the terminal electron acceptor. OmcA was localized to the interface with hematite, while MtrC was more uniformly displayed on the bacterium’s exterior cell surface. Both cytochromes were also found associated with extracellular material.
Bickmore BR, KM Rosso, ID Brown, and SN Kerisit. 2009. "Bond-Valence Constraints on Liquid Water Structure." Journal of Physical Chemistry A 113(9):1847-1857. Abstract The recent controversy about the structure of liquid water pits a new model involving water molecules in relatively stable rings-and-chains structures against the standard model that posits water molecules in distorted tetrahedral coordination. Molecular dynamics (MD) simulations—both classical and ab initio—almost uniformly support the standard model, but since none of them can yet reproduce all the anomalous properties of water, they leave room for doubt. We argue that it is possible to evaluate these simulations by testing them against their adherence to the bond-valence model, a well known, and quantitatively accurate, empirical summary of the behavior of atoms in the bonded networks of inorganic solids. Here we use the results of ab initio molecular dynamics simulations of ice, water, and several solvated aqueous species to show that the valence sum rule (the first axiom of the bond-valence model,) is followed in both solid and liquid bond networks. We then test MD simulations of water, employing several popular potential models, against this criterion and the experimental O-O radial distribution function. It appears that most of those tested cannot satisfy both criteria well, except TIP4P and TIP5P. If the valence sum rule really can be applied to simulated liquid structures, then it follows that the bonding behaviors of atoms in liquids are in some ways identical to those in solids. We support this interpretation by showing that the simulations produce O-H…O geometries completely consistent with the range of geometries available in solids, and the distributions of instantaneous valence sums reaching the atoms in both the ice and liquid water simulations are essentially identical. Taken together, this is powerful evidence in favor of the standard distorted tetrahedral model of liquid water structure.
Windus TL, EJ Bylaska, K Tsemekhman, J Andzelm, and N Govind. 2009. "Computational Nanoscience with NWChem." Journal of Computational and Theoretical Nanoscience 6(6 SP ISS):1297-1304. Abstract The NWChem software as been used to examine many nanoscale systems and their properties over the years. In this paper, an overiew of the general capabilities of NWChem is given as well as more specific details on the planewave and Gaussian based density functional codes usually used for nanoscale investigations. Examples are given of the scientific literature using NWChem, as well as two case studies: 1) Band gaps in oxides using exact-exchange based exchange-correlation functionals with the planewave DFT module, 2) Optical properties of chromophores using the Gaussian based DFT module.
Wang CM, DR Baer, JE Amonette, MH Engelhard, J Antony, and Y Qiang. 2009. "Morphology and Electronic Structure of the Oxide Shell on the Surface of Iron Nanoparticles." Journal of the American Chemical Society 131(25):8824?8832. doi:10.1021/ja900353f Abstract A iron nanoparticle exposed to air at room temperature will be instantly covered by an oxide shell of typical thickness of ~ 3 nm. This native oxide shell in combination with an underlying iron core determines the physical and chemical behavior of this type of core-shell nanoparticles. One of the great challenges for characterizing this type of nanoparticles is determination of the structure of the oxide shell, as it is FeO, Fe3O4, -Fe2O3, -Fe2O3, or anything else. Significant research effort, mostly based on x-ray diffraction and spectroscopy and electron diffraction and transmission electron microscopy imaging, has been made to determine the structure of this thin layer of iron oxide. Most of the experimental results have been framed with one of the known iron oxide structures, although it is not necessarily true that this thin layer of iron oxide consists of a standard iron oxide. In this paper, the structure of the oxide shell on iron nanoparticle is probed using electron energy loss spectroscopy (EELS) at O K-edge with a spatial resolution of several nanometers (individual particle). Two types of representative particles were studied: particles that are fully oxidized and core-shell particle which possesses a Fe core. We found that the O K-edge spectra collected on the oxide shell in the nanoparticles shows distinctive differences as compared with that of the known iron oxide. Based on finger printing and quantum mechanical calculations results, we conclude that the distances between the absorbing oxygen and the next-nearest neighbor oxygens are more widely distributed than that in bulk Fe3O4 for both of these two types of particles. For smaller and fully oxidized particles, there is also a broadened distribution between the absorbing oxygen and the nearest neighbor oxygens. These results clearly demonstrate that the coordination configuration in the oxide shell on Fe nanoparticle is defective as compared with that of their bulk counterpart. Of the two types particles examined in this work, the degree of disorder is larger for the smaller fully oxidized particles.
Zarzycki PP, and KM Rosso. 2009. "Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study." Langmuir 25(12):6841-6848. Abstract Replica Kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface non-uniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation do not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic non-uniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.
Nellis S, H Yoon, C Werth, M Oostrom, and AJ Valocchi. 2009. "Surface and Interfacial Properties of Nonaqueous-Phase Liquid Mixtures Released to the Subsurface at the Hanford Site ." Vadose Zone Journal 8(2):344-351. Abstract Surface and interfacial tensions that arise at the interface between different phases are key parameters affecting Nonaqueous Phase Liquid (NAPL) movement and redistribution in the vadose zone after spill events. In this study, the impact of major additive components on surface and interfacial tensions for organic mixtures and wastewater was investigated. Organic mixture and wastewater compositions are based upon carbon tetrachloride (CT) mixtures released at the Hanford site, where CT was discharged simultaneously with dibutyl butyl phosphonate (DBBP), tributyl phosphate (TBP), dibutyl phosphate (DBP), and a machining lard oil (LO). A considerable amount of wastewater consisting primarily of nitrates and metal salts was also discharged. The tension values measured in this study revealed that the addition of these additive components caused a significant lowering of the interfacial tension with water or wastewater and the surface tension of the wastewater phase in equilibrium with the organic mixtures, compared to pure CT, but had minimal effect on the surface tension of the NAPL itself. These results lead to large differences in spreading coefficients for several mixtures, where the additives caused both a higher (more spreading) initial spreading coefficient and a lower (less spreading) equilibrium spreading coefficient. This indicates that if these mixtures migrate into uncontaminated areas, they will tend to spread quickly, but form a higher residual NAPL saturation after equilibrium, as compared to pure CT. Over time, CT likely volatilizes more rapidly than other components in the originally disposed mixtures and the lard oil and phosphates would become more concentrated in the remaining NAPL, resulting in a lower interfacial tension for the mixture. Spreading coefficients are expected to increase and perhaps change the equilibrated organic mixtures from nonspreading to spreading in water-wetting porous media. These results show that the behavior of organic chemical mixtures should be accounted for in numerical flow and transport models.
Xu Z, P Meakin, and AM Tartakovsky. 2009. "Diffuse-interface model for smoothed particle hydrodynamics." Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 79(3):Art. No. 036702. Abstract Diffuse-interface theory provides a foundation for the modeling and simulation of microstructure evolution in a very wide range of materials, and for the tracking/capturing of dynamic interfaces between different materials on larger scales. Smoothed particle hydrodynamics (SPH) is also widely used to simulate fluids and solids that are subjected to large deformations and have complex dynamic boundaries and/or interfaces, but no explicit interface tracking/capturing is required, even when topological changes such as fragmentation and coalescence occur, because of its Lagrangian particle nature. Here we developed an SPH model for single-two component singletwo- phase fluids that is based on diffuse-interface theory. In the model, the interface has a finite thickness and a surface tension that depend on the coefficient, k, of the gradient contribution to the Helmholtz free energy functional and the density dependent homogeneous free energy. In this model, there is no need to locate the surface (or interface) or to compute the curvature at and near the interface. One- and two-dimensional SPH simulations were used to validate the model.
Wan J, Y Kim, TK Tokunaga, Z Wang, S Dixit, CI Steefel, E Saiz, M Kunz, and N Tamura. 2009. "Spatially Resolved U(VI) Partitioning and Speciation: Implications for Plume Scale Behavior of Contaminant U in the Hanford Vadose Zone." Environmental Science & Technology 43(7):2247-2253. Abstract A saline-alkaline brine containing high concentration of U(VI) was accidentally spilled at the Hanford Site in 1951, introducing 10 tons of U into sediments under storage tank BX-102. U concentrations in the deep vadose zone and groundwater plumes increase with time, yet how the U has been migrating is not fully understood. We simulated the spill event in laboratory soil columns, followed by aging, and obtained spatially resolved U partitioning and speciation along simulated plumes. We found after aging, at apparent steady state, that the pore aqueous phase U concentrations remained surprisingly high (up to 0.022 M), in close agreement with the recently reported high U concentrations (up to 0.027 M) in the vadose zone plume (1). The pH values of aged pore liquids varying from 10 to 7, consistent with the measured pH of the field borehole sediments varying from 9.5 to 7.4 (2), from near the plume source to the plume front. The direct measurements of aged pore liquids together with thermodynamic calculations using a Pitzer approach revealed that UO2(CO3)34- is the dominant aqueousUspecies within the plume body (pH 8-10), whereas Ca2UO2(CO3)3 and CaUO2(CO3)32- are also significant in the plume front vicinity (pH 7-8), consistent with that measured from field borehole pore-waters (3). U solid phase speciation varies at different locations along the plume flow path and even within single sediment grains, because of location dependent pore and micropore solution chemistry. Our results suggest that continuous gravitydriven migration of the highly stable UO2(CO3)34- in the residual carbonate and sodium rich tank waste solution is likely responsible for the detected growing U concentrations in the vadose zone and groundwater.

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