Scientific Publications 2010
2010. "PuPO4(cr, hyd.) Solubility Product and Pu3+ Complexes With Phosphate and Ethylenediaminetetraacetic Acid ." Journal of Solution Chemistry 39(6):778-807. doi:10.1007/s10953-010-9541-x Abstract To determine the solubility product of PuPO4(cr, hyd.) and the complexation constants of Pu(III) with phosphate and EDTA, the solubility of PuPO4(cr, hyd.) was investigated as a function of: 1) time and pH varying from 1.0 to 12.0 and at a fixed 0.00032 M phosphate concentration; 2) NaH2PO4 concentrations varying from 0.0001 M to 1.0 M and at a fixed pH value of 2.5; 3) time and pH varying from 1.3 to 13.0 at fixed concentrations of 0.00032 M phosphate and 0.0004 M or 0.002 M Na2H2EDTA; and 4) Na2H2EDTA concentrations varying from 0.00005 M to 0.0256 M at a fixed 0.00032 M phosphate concentration and at pH values of approximately 3.5, 10.6, and 12.6. A combination of solvent extraction and spectrophotometric techniques confirmed that the use of hydroquinone and Na2S2O4 helped maintain Pu as Pu(III). The solubility data were interpreted using Pitzer and SIT models, and both provided similar values for the solubility product of PuPO4(cr, hyd.) and for the formation constant of PuEDTA-. The log10 of the solubility product of PuPO4(cr, hyd.) (PuPO4(cr, hyd.) = Pu3+ + PO4 ) was determined to be –(24.42 ± 0.38). Pitzer modeling showed that phosphate interactions with Pu3+ were extremely weak and did not require any phosphate complexes (e.g., PuPO4(aq), PuH2PO42+, Pu(H2PO4)2+, Pu(H2PO4)3(aq), and Pu(H2PO4)4-), as proposed in existing literature, to explain the experimental data. SIT modeling, however, required the inclusion of PuH2PO42+ to explain the data in high NaH2PO4 concentrations; this illustrates the differences one can expect when using these two chemical models to interpret the data. As the Pu(III)-EDTA species, only PuEDTA- was needed to interpret the experimental data in a large range in pH values (1.3–12.9) and EDTA concentrations (0.00005–0.256 M). Calculations based on density functional theory support the existence of PuEDTA- (with prospective stoichiometry as Pu(OH2)3EDTA-) as the chemically and structurally stable species. The log10 of the complexation constant for the formation of PuEDTA- [Pu3+ + EDTA4- = PuEDTA-] determined in this study is -20.15 ± 0.59. The data also showed that PuHEDTA(aq), Pu(EDTA)25-, Pu(EDTA)(HEDTA)4-, Pu(EDTA)(H2EDTA)3-, and Pu(EDTA)(H3EDTA)2-, reported in the literature, have no region of dominance in the experimental range of variables investigated in this study.
2010. "Simulating the Heterogeneity in Braided Channel Belt Deposits: Part 1. A Geometric-Based Methodology and Code." Water Resources Research 46():Article Number: W04515 . Abstract A geometric-based simulation methodology was developed and incorporated into a computer code to model the hierarchical stratal architecture, and the corresponding spatial distribution of permeability, in braided channel belt deposits. The code creates digital models of these deposits as a three-dimensional cubic lattice, which can be used directly in numerical aquifer or reservoir models for fluid flow. The digital models have stratal units defined from the km scale to the cm scale. These synthetic deposits are intended to be used as high-resolution base cases in various areas of computational research on multiscale flow and transport processes, including the testing of upscaling theories. The input parameters are primarily univariate statistics. These include the mean and variance for characteristic lengths of sedimentary unit types at each hierarchical level, and the mean and variance of log-permeability for unit types defined at only the lowest level (smallest scale) of the hierarchy. The code has been written for both serial and parallel execution. The methodology is described in Part 1 of this series. In Part 2, models generated by the code are presented and evaluated.
2010. "Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD) ." Analytical and Bioanalytical Chemistry 397:1809-1819. doi:10.1007/s00216-010-3742-4 Abstract Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of morbidity and mortality in the United States and cigarette smoking is a primary determinant of the disease. COPD is characterized by chronic airflow limitation as measured by the forced expiratory volume in one second (FEV1). In this study, the plasma proteomes of 38 middle-aged or older adult smokers with mild to moderate COPD, with FEV1 decline characterized as either rapid (RPD, n = 20) or slow or absent (SLW, n = 18), were interrogated using a comprehensive high-throughput proteomic approach, the accurate mass and time (AMT) tag technology. This technology is based upon a putative mass and time tag database (PMT), high-resolution LC separations and high mass accuracy measurements using FT-ICR MS with a 9.4-T magnetic field. The peptide and protein data were analyzed using three statistical approaches to address ambiguities related to the high proportion of missing data inherent to proteomic analysis. The RPD and SLW groups were differentiated by 55 peptides which mapped to 33 unique proteins. Twelve of the proteins have known roles in the complement or coagulation cascade and, despite an inability to adjust for some factors known to affect lung function decline, suggest potential mechanistic biomarkers associated with the rate of lung function decline in COPD. Whether these proteins are the cause or result of accelerated decline will require further research.
2010. "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota." Microbial Ecology 60(3):539-550. doi:10.1007/s00248-010-9657-y Abstract A microbial census on the deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Mineralogical characterization of soil samples was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated the presence of silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable amount of similar microbial communities (1360 common OTUs) despite of distinct geochemical characteristics. A total of 57 phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity in deep biosphere by capturing several physiological groups of bacteria such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. Application of high-density microarrays revealed the vast prokaryotic diversity ever reported from deep subsurface habitat of gold mines.
2010. "Role of Outer-Membrane Cytochromes MtrC and OmcA in the Biomineralization of Ferrihydrite by Shewanella oneidensis MR-1." Geobiology 8(1):56-68. doi:10.1111/j.1472-4669.2009.00226.x Abstract In an effort to improve the understanding of electron transfer mechanisms at the microbe-mineral interface, Shewanella oneidensis MR-1 mutants with in-frame deletions of outer membrane cytochrome genes mtrC, omcA, or both, were characterized for the ability to reduce metal oxides using a suite of microscopic, spectroscopic, and biochemicalr techniques. The results indicate that neither MtrC nor OmcA are essential for the reduction of soluble, complexed Fe(III)-citrate or Fe(III)-NTA; however, at least one of these outer membrane cytochromes is required for the reduction of Fe(III)- and Mn(III/IV)- oxides. In vitro analysis of purified, recombinant protein demonstrated that both cytochromes transfer electrons directly to metal-oxides; however, MtrC transfers electrons at a faster rate than OmcA. Immunolocalization of MtrC and OmcA reveal that both cytochromes are surface-exposed on the cell outer-membrane and co-localize with insoluble iron precipitates when respiring ferrihydrite or cultured aerobically with Fe(III)-citrate. Additionally, during prolonged incubation, wild-type cells promoted biotransformation of ferrihydrite to vivianite [Fe3(PO4)2•8H2O] while the double cytochrome mutant was unable to form any secondary mineral phases. Collectively, our results support a role for direct electron transfer from OMCs to metal oxides by establishing their in vitro electron transfer activities, confirming the requirement of either MtrC or OmcA for in vivo reductive biomineralization of ferrihydrite, and localizing the cytochromes to the cell exterior where they can directly contact mineral substrates.
2010. "Modeling of Electrochemistry and Steam-Methane Reforming Performance for Simulating Pressurized Solid Oxide Fuel Cell Stacks." Journal of Power Sources 195(19):6637-6644. doi:10.1016/j.jpowsour.2010.04.024 Abstract This paper examines the electrochemical and direct internal steam-methane reforming performance of the solid oxide fuel cell when subjected to pressurization. Pressurized operation boosts the Nernst potential and decreases the activation polarization, both of which serve to increase cell voltage and power while lowering the heat load and operating temperature. A model considering the activation polarization in both the fuel and air electrodes was adopted to address this effect on the electrochemical performance. The pressurized methane conversion kinetics and the increase in equilibrium methane concentration are considered in a new rate expression. The models were then applied in simulations to predict how the distributions of direct internal reforming rate, temperature, and current density are effected within stacks operating at elevated pressure. A generic 10 cm counter-flow stack model was created and used for the simulations of pressurized operation. The predictions showed improved thermal and electrical performance with increased operating pressure. The average and maximum cell temperatures decreased by 3% (20ºC) while the cell voltage increased by 9% as the operating pressure was increased from 1 to 10 atmospheres.
2010. "In Situ Effective Diffusion Coefficient Profiles in Live Biofilms Using Pulsed-Field Gradient Nuclear Magnetic Resonance." Biotechnology and Bioengineering 106(6):928-937. Abstract Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well-documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: 1) invasive to the biofilm, 2) performed under unnatural conditions, 3) lethal to cells, and/or 4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: 1) measure the effective diffusion coefficient for water in live biofilms, 2) monitor how the effective diffusion coefficient changes over time under growth conditions, and 3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (Drs) profiles. We found that 1) Drs decreased from the top of the biofilm to the bottom, 2) Drs profiles differed for biofilms of different ages, 3) Drs profiles changed over time and generally decreased with time, 4) all the biofilms showed very similar Drs profiles near the top of the biofilm, and 5) the Drs profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm.
2010. "Stabilization and Structure Calculations for Noncovalent Interactions inExtended Molecular Systems Based on Wave Function and Density Functional Theories." Chemical Reviews 110(9):5023-5063. doi:10.1021/cr1000173 Abstract More than 20 years ago, we published in Chemical Reviews a paper entitled “Intermolecular Interactions between Medium-Sized Systems. Nonempirical and Empirical Calculations of Interaction Energy: Successes and Failures”. The situation in calculations of noncovalent interactions at that time can be best characterized by the question we posed at the very beginning of the review: “Can quantum chemistry describe vdW (van der Waals; today we call it noncovalent) interactions as successfully as covalent interactions?” Our answer then was “unambiguously yes”. We had good reason for an optimistic “yes” since we presented the first coupledcluster calculations including triple excitations for a (at that time) large complexsthe water dimer. We stressed the importance of the triple excitations for noncovalent interactions, and in the section called Prospects, we wrote that “significant progress is highly desirable with beyond-SCF methods, where new, more accurate and efficient procedures are developed”. In this respect we were right, and in the past 20 years, we have witnessed an enormous growth of interest in the fast and accurate calculation of intermolecular interactions. What is the reason for such an interest, or more generally, why are noncovalent interactions so relevant in modern research? Is it the mere existence of noncovalent complexes in the gas and liquid phases? Certainly not. The answer should be sought in the role that noncovalent interactions are playing in both bio- and nanostructures.
2010. "Molecular Characterization of Organic Aerosols Using Nanospray Desorption/Electrospray Ionization-Mass Spectrometry." Analytical Chemistry 82(19):7979–7986. doi:10.1021/ac101449p Abstract Nanospray desorption electrospray ionization (Nano-DESI) combined with high-resolution mass spectrometry (HR/MS) is a promising approach for detailed chemical characterization of atmospheric organic aerosol (OA) collected in laboratory and field experiments. In Nano-DESI analyte is desorbed into a solvent bridge formed between two capillaries and the analysis surface, which enables fast and efficient characterization of OA collected on substrates without special sample preparation. Stable signals achieved using Nano-DESI make it possible to obtain high-quality HR/MS data using only a small amount of material (<10 ng). Furthermore, Nano-DESI enables efficient detection of chemically labile compounds in OA, which is important for understanding chemical aging phenomena.
2010. "Nanospray Desorption Electrospray Ionization: an Ambient Method for Liquid-Extraction Surface Sampling in Mass Spectrometry." Analyst 135(9):2233-2236. Abstract A novel nanospray desorption electrospray ionization (nano-DESI) approach is presented and its analytical applications are demonstrated for trace analysis of complex organic analytes deposited on substrates. In this approach the analyte is probed by a micro-droplet of charged solvent formed at the junction between two capillaries. One primary capillary is used to create and maintain a charged micro-droplet of solvent on the substrate while a second capillary is used to create a self-aspirating nanospray that delivers solvent dissolved analyte to the inlet of a mass spectrometer. This approach enables efficient separation of desorption and ionization events, thus providing better control over transport and ionization of the analyte. In this letter we present the basics of the nano-DESI approach and demonstrate its analytical capabilities. Specifically, we demonstrate significant improvement of the limits of detection and the stability of the signal as compared to the traditional DESI and discuss imaging applications.
2010. "Transport of Strontium and Cesium in Simulated Hanford Tank Waste Leachate through Quartz Sand under Saturated and Unsaturated Flow ." Environmental Science & Technology 44(21):8089-8094. doi:10.1021/es903223x Abstract We investigated the effects of water saturation and formation of secondary precipitates on transport of Sr and Cs through sand columns under unsaturated water flow. A series of column experiments was run at effective water saturations ranging from 0.2 to 1.0 under steady-state flow using columns filled with quartz sand. The solution phase was either 0.1 M NaNO3 or a simulated tank waste leachate (STWL), mimicking the leaks of tank wastes at the Hanford Site, Washington, USA. In STWL, the mobility of Sr was significantly reduced as the water saturation decreased, because Sr was incorporated into or sorbed to neo-formed secondary precipitates. In contrast, the transport of Cs in STWL was similar to that of a nonreactive tracer. In 0.1 M NaNO3, Sr moved like a conservative tracer, showing no retardation, whereas Cs was retarded relative to Sr. The flow regime for the 0.1 M NaNO3 columns under all water saturations could be described with the equilibrium convection-dispersion equation (CDE). However, for STWL, the Sr and Cs breakthrough curves indicated the presence of non-equilibria under unsaturated flow conditions. Such non-equilibrium conditions, caused by physical and chemical processes can reduce the mobility of radionuclides at the Hanford vadose zone.
2010. "Connecting Observations of Hematite (a Fe2O3) Growth Catalyzed by Fe(II)." Environmental Science & Technology 44(1):61-67. Abstract Electron exchange between aqueous Fe(II) and structural Fe(III) in iron oxides and oxyhydroxides is important for understanding degradation of environmental pollutants through its apparent constitutive role underlying highly reactive “sorbed Fe(II)” and by catalyzing phase interconversion among these minerals. Although a mechanistic understanding of relationships between interfacial Fe(II)ads-Fe(III)oxide electron transfer, bulk electron conduction, and phase transformation behavior is emerging, much remains unclear in part due to poorly interconnected investigations. The focus of this study is on reconciling two mutually similar observations of Fe(II)-catalyzed hematite growth documented spectroscopically and microscopically under substantially different chemical conditions. Here we employ iron isotopic labeling to demonstrate that hematite grown on the (001) surface in Fe(II)-oxalate solution at low pH and elevated temperature has temperature-dependent magnetic properties that closely correspond to those of hematite grown in Fe(II) solution at circumneutral pH at room temperature. The temperature evolution and extent of the Morin transition displayed in these two materials strongly suggest a mechanistic link between the two studies, and that this mechanism involves in part trace structural Fe(II) incorporation into the growing hematite. Our findings indicate that Fe(II) catalyzed growth of hematite on hematite can occur under environmentally relevant conditions and may be due to bulk electron conduction previously demonstrated for hematite single crystals.
2010. "Calculation of boron-isotope fractionation between B(OH)(3)(aq) and B(OH)(4)(-)(aq)." Geochimica et Cosmochimica Acta 74(10):2843-2850. doi:10.1016/j.gca.2010.02.032 Abstract Density functional and correlated molecular orbital calculations (MP2) are carried out on B(OH)3-nH2O clusters (n = 0, 6,32), and B(OH)-4.nH20 (n = 0, 8, 11, 32) to estimate the equilibrium distribution of 10B and 11B isotopes between boric acid and borate in aqueous solution. For the large 32-water clusters, multiple conformations are generated from ab initio molecular dynamics simulations to account for the effect of solvent fluctuations on the isotopic fractionation. We provide an extrapolated value of the equilibrium constant x34 for the isotope exchange reaction 10B(OH)3(aq) + 11B(OH)-4 (aq) = 11B(OH)3(aq) + 11B(OH)-4 (aq) of 1.026-1.028 near the MP2 complete basis set limit with 32 explicit waters of solvation. With some exchange-correlation functionals we find potentially important contributions from a tetrahedral neutral B(OH)3.H2O Lewis acid-base complex. The extrapolations presented here suggest that DFT calculations give a value for 103lnx34 about 15% higher than the MP2 calculations.
2010. "Isotopic Fractionation of Mg2+(aq), Ca2+(aq), and Fe2+(aq) with Carbonate Minerals." Geochimica et Cosmochimica Acta 74(22):6301-6323. Abstract Density functional electronic structure calculations are used to compute the equilibrium constant (the isotope fractionation factor) for 26Mg/24Mg and 44Ca/40Ca isotope exchange between carbonate minerals and uncomplexed divalent aquo ions. The most reliable calculations at the B3LYP/6-311++G(2d,2p) level predict equilibrium constants K, reported as 103ln(K) at 25 °C, of -5.3, -1.1, and +1.1 for 26Mg/24Mg exchange between calcite (CaCO3), magnesite (MgCO3), and dolomite (Ca0.5Mg0.5CO3), respectively, and Mg2+(aq), with positive values indicating enrichment in the mineral phase. For 44Ca/40Ca exchange between calcite and Ca2+(aq), the calculations predict values of +1.5 for Ca2+(aq) in six-fold coordination and +4.1 for Ca2+(aq) in seven-fold coordination. We find that the reduced partition function ratios can be reliably computed from systems as small as M(CO3)610- and M2+(H2O)6 embedded in a set of fixed atoms representing the 2nd shell (and greater) coordination environment. We find that the aqueous cluster representing the aquo ion is much more sensitive to improvements in the basis set than the calculations on the mineral systems, and that fractionation factors should be computed using 2 the best possible basis set for the aquo complex, even if the reduced partition function ratio calculated with the same basis set is not available for the mineral system. The new calculations show that the previous discrepancies between theory and experiment for Fe3+-hematite and Fe2+-siderite fractionations arise from an insufficiently accurate reduced partition function ratio for the Fe3+(aq) and Fe2+(aq) species.
2010. "Thiol-Ene Induced Diphosphonic Acid Functionalization of Superparamagnetic Iron Oxide Nanoparticles." Langmuir 26(14):12285-12292. Abstract Multi-functional organic molecules represent an interesting challenge for nanoparticle functionalization due to the potential for undesirable interactions between the substrate material and the variable functionalities, making it difficult to control the final orientation of the ligand. In the present study, UV-induced thiol-ene click chemistry has been utilized as a means of directed functionalization of bifunctional ligands on an iron oxide nanoparticle surface. Allyl diphosphonic acid ligand was covalently deposited on the surface of thiol-presenting iron oxide nanoparticles via the formation of a UV-induced thioether. This method of thiol-ene click chemistry offers a set of reaction conditions capable of controlling the ligand deposition and circumventing the natural affinity exhibited by the phosphonic acid moiety for the iron oxide surface. These claims are supported via a multimodal characterization platform which includes thermogravimetric analysis, x-ray photoelectron spectroscopy, and metal contact analysis and are consistent with a properly oriented, highly active ligand on the nanoparticle surface. These experiments suggest thiol-ene click chemistry as both a practical and generally applicable strategy for the directed deposition of multi-functional ligands on metal oxide nanoparticle surfaces.