Scientific Publications 2010
2010. "Uranium(VI) Reduction by Nanoscale Zerovalent Iron in Anoxic Batch Systems." Environmental Science & Technology 44(20):7783-7789. doi:10.1021/es9036308 Abstract This study investigated the influences of pH, bicarbonate, and calcium on U(VI) adsorption and reduction by synthetic nanosize zero valent iron (nano Fe0) particles under an anoxic condition. The results showed that about 87.1%, 82.7% and 78.3% of U(VI) could be reduced within 96 hours in the presence of 10 mM bicarbonate at pHs 6.92, 8.03 and 9.03, respectively. The rates of U(VI) reduction and adsorption by nano Fe0, however, varied significantly with increasing pH and concentrations of bicarbonate and/or calcium. Solid phase analysis by X-ray photoelectron spectroscopy confirmed the formation of UO2 and iron (hydr)oxides as a result of the redox interactions between adsorbed U(VI) and nano Fe0. This study highlights the potential important role of groundwater chemical composition in controlling the rates of U(VI) reductive immobilization using nano Fe0 in subsurface environments.
2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152. doi:10.1371/journal.pone.0014152 Abstract Background: High doses of ionizing radiation result in biological damage, however the precise relationships between long term health effects, including cancer, and low dose exposures remain poorly understood and are currently extrapolated using high dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose dependent responses to radiation. Principle Findings: We have identified 6845 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts one hour post-exposure. Dual statistical analyses based on spectral counts and peak intensities identified 287 phosphopeptides (from 231 proteins) and 244 phosphopeptides (from 182 proteins) that varied significantly following exposure to 2 and 50 cGy respectively. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatics analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role of MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conlcusions: Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provides a basis for the systems level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low dose radiation exposure on human health.
2010. "Hydrogen Oxidation Catalysis by a Nickel Diphosphine Complex with Pendant tert-Butyl Amines." Chemical Communications 46:8618-8620. doi:10.1039/C0CC03246H Abstract A bis-diphosphine nickel complex with t-butyl functionalized pendant amines [Ni(PCy2Nt-Bu2)2]2+ has been synthesized. It is a highly active electrocatalyst for the oxidation of hydrogen in the presence of base. The turn-over rate of 50 s 1 under 1.0 atm H2 at a potential of –0.77 V vs the ferrocene couple is 5 times faster than the rate reported heretofore for any other molecular H2 oxidation catalyst. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. Computational resources were provided by the Environmental Molecular Science Laboratory (EMSL) and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.
2010. "(Non) formation of methanol by direct hydrogenation of formate on copper catalysts." Journal of Physical Chemistry C 114(40):17205-17211. doi:10.1021/jp104068k Abstract We have attempted to hydrogenate adsorbed formate species on copper catalysts to probe the importance of this postulated mechanistic step in methanol synthesis. Surface formate coverages up to 0.25 were produced at temperatures between 413K and 453K on supported (Cu/SiO2) copper and unsupported copper catalysts. The adlayers were produced by various methods including (1) steady state catalytic conditions in CO2-H2 (3:1, 6 bar) atmospheres, and (2) by exposure of the catalysts to formic acid. As reported in earlier work, the catalytic surface at steady state contains bidentate formate species with coverages up to saturation levels of ~ 0.25 at the low temperatures of this study. The reactivity of these formate adlayers was investigated at relevant reaction temperatures in atmospheres containing up to 6 bar H2 partial pressure by simultaneous mass spectrometry (MS) and infrared (IR) spectroscopy measurements. The yield of methanol during the attempted hydrogenation (“titration”) of these adlayers was insignificant (<0.2 mol % of the formate adlayer) even in dry hydrogen partial pressures up to 6 bar. Hydrogen titration of formate species produced from formic acid also failed to produce significant quantities of methanol, and attempted titration in gases consisting of CO-hydrogen mixtures or dry CO2 were also unproductive. The formate decomposition kinetics, measured by IR, were also unaffected by these changes in the gas composition. Similar experiments on unsupported copper also failed to show any methanol. From these results, we conclude that methanol synthesis on copper cannot result from the direct hydrogenation of (bidentate) formate species in simple steps involving adsorbed H species alone. Furthermore, experiments performed on both supported (Cu/SiO2) and unsupported copper catalysts gave similar results implying that the methanol synthesis reaction mechanism only involves metal surface chemistry. Pre-exposure of the bidentate formate adlayer to oxidation by O2 or N2O produces a change to a monodentate configuration. Attempted titration of this monodentate formate/O coadsorbed layer in dry hydrogen produces significant quantities of methanol, although decomposition of formate to carbon dioxide and hydrogen remains the dominant reaction pathway. Simultaneous production of water is also observed during this titration as the copper surface is re-reduced. These results indicate that co-adsorbates related to surface oxygen or water-derived species may be critical to methanol production on copper, perhaps assisting in the hydrogenation of adsorbed formate to adsorbed methoxyl.
2010. "Combining NMR, PRE, and EPR Methods For Homodimer Protein Structure Determination." Journal of the American Chemical Society 132(34):11910-11913. doi:10.1021/ja105080h Abstract Homo-oligomer and multi-protein complex structure determination using solution NMR methods usually relies on inter-chain NOEs detected by X-filtered NOE experiments.1,2 These techniques, which require preparation of mixed isotopically labeled and unlabeled samples, are often not sensitive or difficult to interpret due to imperfect artifact suppression. Under the worst conditions, these methods can fail to provide unambiguous inter-chain NOEs, as was the case for Northeast Structural Genomics Consortium (NESG) target DhR8C, a homo-dimer of 62 residues. For Dh8rC, only a few unambiguous inter-chain 13C-edited/12C-filtered NOEs were detected, indicating potential problems including 1) tight dimer association resulting unfavorable chain exchange kinetics and a low population of mixed 13C/12C-labeled chains, 2) weak dimer association preventing measurement of inter-chain NOEs, or 3) a dimer interface whose nature prevented measurement or interpretation of inter-chain NOEs. This problem hindered the DhR8C homo-dimer structure determination using NMR methods alone.
2010. "Solution NMR Structure of Photosystem II Reaction Center Protein Psb28 from Synechocystin sp. Strain PCC 6803." Proteins. Structure, Function, and Bioinformatics 79(1):340-344. doi:10.1002/prot.22876 Abstract Oxygenic photosynthesis is initiated by photosystem II (PSII) in the thylakoid membranes of plants, algae and cyanobacteria. PSII is a multi-subunit pigment-protein complex responsible for splitting water into oxygen gas, hydrogen ions, and electrons transferred to electron acceptors during photosynthesis.1 Two homologous membrane-spanning proteins D1 (PsbA) and D2 (PsbD) form the PSII complex core.1 Peripherally, two chlorophyll (Chl)-binding inner antenna proteins CP47 (PsbB) and CP43 (PsbC) are bound to the D1-D2 PSII complex core.1 These four large proteins are surrounded by a large number of smaller membrane proteins.2 Most of these small proteins have been observed in the crystal structures of the PSII complex from cyanobacteria.3,4 However, one small protein, Psb28, previously detected as a nonstoichiometric component of PSII,5 was not observed in the crystal structures indicating that Psb28 might not be a true PSII subunit. Recent studies revealed that Psb28 was preferentially bound to PSII core complex lacking CP43 (RC47) and involved in the biogenesis of CP47.6 Understanding the association of Psb28 to PSII core complex should provide additional insight into its role in PSII function, however, the structure of Psb28 remains unknown. In this note, we report the solution NMR structure of Psb28 protein encoded by gene sll1398 [gi|952386] of Synechocystis sp. strain PCC 6803(SWISS-PROT ID: PSB28_SYNY3, NESG target ID: SgR171).7 This protein, also named Psb13 or ycf79, belongs to the Psb28 protein family (Pfam ID: PF03912), which is currently made up of ~48 protein sequences. Both PSI-BLAST and Dali8 searches indicated this is the first atomic resolution structure available for the Psb28 family. ConSurf9 was used to identify conserved residues potentially involved in binding to the PSII core complex.10
2010. "Functional Sorbents for Selective Capture of Plutonium, Americium, Uranium, and Thorium in Blood." Health Physics 99(3):413-419. Abstract Nano-engineered solid sorbents for chelation of actinides (239Pu, 241Am, uranium, thorium) from human blood were developed and evaluated in vitro. These sorbents, known as the self-assembled monolayer on mesoporous supports (SAMMSTM), are hybrid materials created from attachment of organic moieties onto extremely high surface area mesoporous silica. The organic moieties known to be effective at capturing actinides including three isomers of hydroxypyridinone, diphosphonic acid, acetamide phosphonic acid, glycinyl urea, and diethylenetriamine pentaacetate analog were evaluated. SAMMS are being reported elsewhere as potential candidates for orally administered drug for radionuclide decorporation. Herein, actinide decorporation of SAMMS in blood were evaluated to assess their viability for sorbent hemoperfusion in renal insufficient patients, whose kidney clear radionuclides at very slow rate. Sorption affinity (Kd), sorption rate, selectivity, and stability of SAMMS were measured in batch contact experiments. An isomer of hydroxypyridinone (3,4-HOPO) on SAMMS demonstrated the highest affinity for decorporation of all four actinides and outperformed the DTPA analog on SAMMS and on commercial resins by a factor of 103-fold in term of affinity. A fifty percent reduction of actinides in blood was achieved within minutes with no evidence of protein fouling and material leaching in blood after 24 hr of contact time. Less than 0.4 wt.% of Si was dissolved from 3,4-HOPO-SAMMS across the pH of 0 to 8. The engineered form of SAMMS (bead format) was further evaluated in a 100-fold scaled-down hemoperfusion device and showed no blood clotting after 2 hr. A 0.2 g of SAMMS could reduce 50 wt.% of 100 ppb uranium in 50 mL of plasma in just 18 min and that of 500 dpm mL-1 in just 24 min. 3,4-HOPO-SAMMS has a long shelf-life in air and at room temperature for at least 8 years, indicating their feasibility for stockpiling in preparedness for emergency.
2010. "Functionalized Nanoporous Silica for Removal of Heavy Metals from Biological Systems; Adsorption and Application." ACS Applied Materials & Interfaces 2(10):2749-2758. doi:10.1021/am100616b Abstract Functionalized nanoporous silica, often referred to as self-assembled monolayers on mesoporous supports (SAMMS) have previously demonstrated the ability to serve as very effective heavy metal sorbents in a range of aquatic and environmental systems suggesting they may be advantageously utilized for biomedical applications such as chelation therapy. Herein we evaluate surface chemistries for heavy metal capture from biological fluids, various facets of the materials biocompatibility and the suitability of these materials as potential therapeutics. Of the materials tested, thiol-functionalized SAMMS proved most capable of removing selected heavy metals from biological solutions (i.e. blood, urine, etc.) As a result, thiol SAMMS was further analyzed to assess the material’s performance under a number of different biologically relevant conditions (i.e. variable pH and ionic strength) as well to gauge any potentially negative cellular effects resulting from interaction with the sorbent, such as cellular toxicity or possible chelation of essential minerals. Additionally, cellular uptake studies demonstrated no cell membrane permeation by the silica-based materials generally highlighting their ability to remain cellularly inert and thus non-toxic. As a result, it has been determined that organic ligand-functionalized nanoporous silica materials could be a valuable material for detoxification therapeutics and potentially other biomedical applications as needed.
2010. "Novel sorbents for removal of gadolinium-based contrast agents in sorbent dialysis and hemoperfusion: preventive approaches to nephrogenic systemic fibrosis ." Nanomedicine 6(1):1-8. doi:10.1016/j.nano.2009.05.002 Abstract Gd based contrast agents in many forms of organocomplex have recently been linked to a debilitating and a potentially fatal skin disease called Nephrogenic Systemic Fibrosis (NSF) in patients with renal failures. Free Gd released from the complexes by transmetallation is believed to be the most important trigger for NSF. Removal of Gd complex from the patients immediately after the contrast study would prevent the dissociation of Gd and should eliminate NSF as a complication. Although removal of Gd based contrast agents may be accomplished with conventional hemodialysis, it requires three hemodialysis sessions at 3 hours each to remove 98% of the contrast agents. In this work, mesoporous silica material that are functionalized with 1-hydroxy-2-pyridinone (1,2-HOPO-SAMMS®) has been evaluated for effective removal of both free and chelated Gd (Magnevist, a brand of gadopentetate dimeglumine) from the dialysate and sodium chloride solution. The material has high affinity, rapid removal rate, and large sorption capacity for both free and chelated Gd, the properties that are far superior to those of activated carbon and zirconium phosphate currently used in the state-of-the-art sorbent dialysis systems. 99% of both free and chelated Gd would be removed in a single pass thru the sorbent bed of 1,2-HOPO-SAMMS®. The sorbent provides an effective and predicable strategy for removing Gd from patients with impaired renal function, thus it would allow for the continued use of contrast MRI while removing the risk of NSF and would represent a safe alternative to traditional contrast studies in the patient population.
2010. "Formation and Luminescence Phenomena of LaF3:Ce3+ Nanoparticles and Lanthanide-Organic Compounds in Dimethyl Sulfoxide." Journal of Physical Chemistry C 114(2):826-831. doi:10.1021/jp9092173 Abstract LaF3:Ce3+ doped nanoparticles were synthesized at different temperatures in dimethyl sulfoxide by the chemical reaction of lanthanum nitrate hydrate and cerium nitrate hexahydrate with ammonium fluoride. The formation of Ce3+ doped LaF3 nanoparticles is confirmed by X-ray diffraction and high resolution transmission electron microscopy. An intense emission at around 310 nm from the d - f transition of Ce3+ was observed from the LaF3:Ce3+ powder samples. However, in solution samples, the ultraviolet emission from Ce3+ is mostly absent, but intense luminescence is observed in the visible range from blue to red. The emission wavelength of the solution samples is dependent on the reaction time and temperature. More interestingly, the emission wavelength varies with the excitation wavelength. Most likely, this emission is from the metalorganic compounds of Ce3+ or La3+ and DMSO as similar phenomena are also observed when lanthanum nitrate hydrate or cerium nitrate hexahydrate are heated in DMSO.
2010. "Luminescence Enhancement of CdTe Nanostructures in LaF3:Ce/CdTe Nanocomposites." Journal of Applied Physics 108(10):207-213. doi:10.1063/1.3506416 Abstract Radiation detection demands new scintillators with high quantum efficiency, high energy resolution and short luminescence lifetimes. Nanocomposites consisting of quantum dots and Ce3+ doped nanophosphors may be able to meet these requirements. Here we report the luminescence of LaF3:Ce/CdTe nanocomposites which were synthesized by a wet chemistry method. In LaF3:Ce/CdTe nanocomposites the CdTe quantum dots are converted into nanowires, while in LaF3/CdTe nanocomposites no such conversion is observed. The CdTe luminescence in LaF3:Ce/CdTe nanocomposites is enhanced about 5 times, while in LaF3/CdTe nanocomposites no enhancement was observed. Energy transfer, light-re-absorption and surface passivation are likely the reasons for the luminescence enhancement.
2010. "Problems with Some Current Water Models for Close Pair Interactions That Are Not Near the Minimum Energy." Journal of Chemical Theory and Computation 6(2):438-442. doi:10.1021/ct900447n Abstract The ability of an empirical, polarizable model of water to predict a thermal ensemble of molecular configurations at ambient conditions was examined using first-principle quantum mechanics. The empirical model of water selected for this evaluation was the TTM2-F model. The quantum mechanical methodology selected was the second-order Møller-Plesset model (MP2). Only pairwise interaction energies were considered. Significant deviations from the empirical model were found. Similar results were found for ad-hoc comparisons with several other common water models including the TIP3P, TIP4P, TIP4P-FQ, TIP5P, TTM2.1-F, TTM2.2- F, TTM3-F, and POL5/QZ potential models. Our results show that spatially close dimer configurations with interaction energies notably above the potential well minimum (but are still thermally accessible at ambient conditions) are the source of the largest deviations. To assist others in future water model parametrizations we report the MP2 near complete basis set limit energies for 840 water dimer configurations sampled from an approximate thermal ensemble at ambient conditions.
2010. "High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16." The Journal of Physical Chemistry Letters 1(20):3122-3127. doi:10.1021/jz101245s Abstract The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at the MP2 and CCSD(T) levels of theory and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17 the CCSD(T) calculations confirm the previously found at the MP2 level of theory "interior" arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum.
2010. "Fast Time-Resolved Aerosol Collector: Proof of Concept." Atmospheric Measurement Techniques 3:1377-1384. doi:10.5194/amt-3-1377-2010 Abstract Atmospheric particles can be collected in the field on substrates for subsequent laboratory analysis via chemically sensitive single particle methods such as scanning electron microscopy with energy dispersed x-ray analysis. With moving substrates one can achieve time resolution of seconds to minutes. We demonstrate how to increase the time resolution to a few milliseconds to provide real-time information in this paper. Our fast time-resolved aerosol collector (“Fast-TRAC”) microscopically observes the particle collection on substrate and record an on-line video. Particle arrivals are resolved to within a single frame (17 to 4 ms in this setup), and the spatial locations are matched to the subsequent single particle analysis. This approach provides real-time information on particle size and number concentration. Applications are expected in airborne studies of cloud microstructure, pollution plumes, and long term site monitoring.
2010. "Integrated Experimental and Modeling Study of Ionic Conductivity of Scandia-Stabilized Zirconia Thin Films." Solid State Ionics 181(8-10):367-371. doi:10.1016/j.ssi.2010.01.024 Abstract Scandia-stabilized zirconia films were epitaxially grown on sapphire (0001) substrates by oxygen-plasma-assisted molecular beam epitaxy. The cubic phase was found to exist over a wider dopant concentration range than previously observed (4.6-17.6 mol% Sc2O3). The monoclinic phase was observed for dopant concentrations of 1.5 mol% and 22.5 mol %. An increase in the fraction of the monoclinic phase relative to the cubic phase decreased the ionic conductivity. The highest conductivity in the temperature range of 460-900 °C was observed for 9.9 mol % Sc2O3. Atomistic computer simulations show that the observed composition dependence can be related to changes in migration barriers for O2- ion transport with Sc3+ substitution of Zr4+ ions.