Scientific Publications 2010
2010. "Molecular Dynamics Simulation of the AgCl/Electrolyte Interfacial Capacity." Journal of Physical Chemistry C 114(21):10019-10026. doi:10.1021/jp100074h Abstract Molecular dynamics simulation of the AgCl/KCl(aq) interfacial electrostatic capacity is presented. The simulations are motivated by the need to reduce ambiguities in the parameterization of conventional electrical double layer models, which here we attempt by determining the interfacial structure and charge distribution explicitly at the molecular level. Reduction of the interfacial molecular structure to conventional fixed plane models of the electrical double layer is shown. The calculated value of interfacial capacity ( F/cm2) is in agreement with experiment for the closely related AgI/electrolyte interface . Capacity profiles determined by combining the molecularly-resolved interfacial structure and hypothetical planes of charge separation show a similar decay to the classical Helmholtz model. This proves that a rigid parallel-plate capacitor model gives a reasonable approximation of the interfacial capacity for the particular electrolyte concentration under consideration (0.72 mol/dm3). Furthermore, the dielectric constant for the first layer of adsorbed water is calculated to equal 5.1, which confirms that water near the charged interface is under dielectric saturation conditions.
2010. "Molecular Dynamics Study of the Electrical Double Layer at Silver Chloride Electrolyte Interfaces." Journal of Physical Chemistry C 114(19):8905-8916. Abstract Molecular dynamics simulations of the electrical double layer at AgCl/aqueous electrolyte (KCl) interfaces are presented, accompanied by a new force field and properties of bulk AgCl computed using planewave density functional theory. Long dynamics simulations were performed to estimate ion adsorption free energies at the AgCl surface. The simulations demonstrate formation of a bilayer hydration sheet composed of two sublayers of water molecules interconnected by hydrogen bonds. Potassium ions prefer to form an inner-sphere complex, whereas chloride ions prefer outer-sphere complexes. The adsorbed ions/water layers form a relatively rigid structure within the range of ionic strength considered, which confirms the applicability of the Helmholtz model in a high concentration regime. Profiles of the charge density, electric field and electrostatic potential across the simulation cell revealed that oscillations of water molecules govern these quantities. The electrostatic potential generated only by the electrolyte ions was used to study the quasi-Nernstian response of the silver chloride surface to the variation in the ionic strength.
2010. "Theory, experiment and computer simulation of the electrostatic potential at crystal/electrolyte interfaces ." Croatia Chemica Acta 83(4):457-474. Abstract In this feature article we discuss recent advances and challenges in measuring, analyzing and interpreting the electrostatic potential development at crystal/electrolyte interfaces. We highlight progress toward fundamental understanding of historically difficult aspects, including point of zero potential estimation for single faces of single crystals, the non-equilibrium pH titration hysteresis loop, and the origin of nonlinearities in the titration response. It has been already reported that the electrostatic potential is strongly affected by many second order type phenomena such as: surface heterogeneity, (sub)surface transformations, charge transfer reactions, and additional potential jumps at crystal face edges and/or Schottky barriers. Single-crystal electrode potentials seem particularly sensitive to these phenomena, which makes interpretation of experimental observations complicated. We hope that recent theory developments in our research group including an analytical model of titration hysteresis, a perturbative surface potential expansion, and a new surface complexation model that incorporates charge transfer processes will help experimental data analysis, and provide unique insights into the electrostatic response of nonpolarizable single-crystal electrodes.
2010. "Nighttime chemical evolution of aerosol and trace gases in a power plant plume: Implications for secondary organic nitrate and organosulfate aerosol formation, NO₃ radical chemistry, and N₂O₅ heterogeneous hydrolysis." Journal of Geophysical Research. D. (Atmospheres) 115:Art. No. D12304. doi:10.1029/2009JD013250 Abstract Chemical evolution of aerosols and trace gases in the Salem Harbor power plant plume was monitored with the DOE G-1 aircraft on the night of July 30-31, 2002. Quasi-Lagrangian sampling in the plume at increasing downwind distances/processing times was guided by a constant-volume tetroon that was released near the power plant at sunset. While no evidence of fly ash particles was found, concentrations of particulate organics, sulfate, and nitrate were higher in the plume than in the nearby background air. These species were internally mixed and the particles were acidic, suggesting that particulate nitrate was in the form of organic nitrate. The enhanced particulate organic and nitrate masses in the plume were inferred to be as secondary organic aerosol, possibly formed from the NO3 radical-initiated oxidation of isoprene and other trace organic gases in the presence of acidic sulfate particles. The enhanced particulate sulfate concentrations observed in the plume were attributed to direct emissions of gaseous SO3/H2SO4 from the power plant. Furthermore, concentration of nucleation mode particles was significantly higher in the plume than in background air, suggesting that some of the emitted H2SO4 had nucleated to form new particles. Spectromicroscopic analyses of particle samples suggested that some sulfate was likely in the form of organosulfates. Constrained Lagrangian model analysis of the aircraft and tetroon observations showed that heterogeneous hydrolysis of N2O5 was negligibly slow. These results have significant implications for several scientific and regulatory issues related to the impacts of power plant emissions on atmospheric chemistry, air quality, visibility, and climate.
2010. "Photochemistry of 1,1,1-Trifluoroacetone on Rutile TiO2(110)." Journal of Physical Chemistry C 114(40):16900-16908. Abstract The ultraviolet (UV) photon-induced photodecomposition of 1,1,1-trifluoroacetone (TFA) adsorbed on the rutile TiO2(110) surface has been investigated with photon stimulated desorption (PSD), temperature programmed desorption (TPD) and density functional theory (DFT). TFA adsorbed molecularly on the reduced surface (8% oxygen vacancies) in states desorbing below 300 K with trace thermal decomposition observed in TPD. Adsorption of TFA on a preoxidized TiO2(110) surface (accomplished by pre-exposure with 20 L O2) led to formation of a new TFA desorption state at 350 K, assigned to decomposition of a TFA-diolate species ((CF3)(CH3)COO). No TFA photochemistry was detected on the reduced surface. UV irradiation of TFA on the oxidized surface depleted TFA in the 350 K state, with TFA molecules in other TPD states unaffected. PSD measurements reveal that both carbonyl substituents (CH3 and CF3), as well as CO, were liberated during UV exposure at 95 K. Post-irradiation TPD showed evidence for both acetate (evolving as ketene at 650 K) and trifluoroacetate (evolving as CO2 at 600 K) as surface-bound photodecomposition products. The CO PSD product was not due to adsorbed CO, to mass spectrometer cracking of a CO-containing PSD product, or from background effects, but originated from complete fragmentation of an unidentified adsorbed TFA species. Thermodynamic analysis using DFT indicated that the photodecomposition of the TFA-diolate was likely not driven by thermodynamics alone as both pathways (CH3+trifluoroacetate and CF3+acetate) were detected when thermodynamics shows a clear preference for only one (CF3+acetate). These observations are in contrast to the photochemical behavior of acetone, butanone and acetaldehyde on TiO2(110), where only one of the two carbonyl substituent groups was observed, with a stoichiometric amount of carboxylate containing the other substituent left on the surface. We conclude that fluorination significantly alters the electronic structure of adsorbed carbonyls on TiO2(110) in such a way as to promote multiple channels of photofragmentation. Factors that dictate the partitioning between the three TFA channels are not related to photon energy (above that of the TiO2 band gap), but likely to the electronic structure of the charge transfer excited state.
2010. "Thermal chemistry and photochemistry of hexafluoroacetone on rutile TiO2(110) ." Physical Chemistry Chemical Physics. PCCP 12(28):8084-8091. Abstract The ultraviolet (UV) photon-induced decomposition of hexafluoroacetone (HFA) adsorbed on the rutile TiO2(110) surface was investigated using photon stimulated desorption (PSD) and temperature programmed desorption (TPD). The initial 0.2 ML coverage of HFA decomposed when adsorbed on the reduced TiO2(110) surface resulting in the formation of trifluoroacetate (evolving in TPD as CO, CO2, and C2F4 near 600 K). Further HFA exposure resulted in molecular adsorption. No evidence for photochemistry was observed on the reduced surface. HFA adsorbed and desorbed molecularly on a pre-oxidized TiO2(110) surface with only a minor amount (~1%) of thermal decomposition in TPD. A new adsorption state at 350 K was assigned to the reversible formation of a photoactive HFA-diolate species [(CF3)2COO]. UV irradiation depleted the 350 K state and resulted in the formation of surface bound trifluoroacetate. PSD experiments showed that CF3, CO, and CO2 were evolved during irradiation at 95 K. Post-irradiation TPD showed evidence for trifluoroacetate (desorbing as CO, CO2, and C2F4 near 600 K) as surface-bound photodecomposition products. 18O isotope scrambling experiments showed that the origin of the ejected CO2 was from photodecomposition of the HFA-diolate species. CO photodesorption was due to an as-yet unidentified adsorbed HFA species and not due to decomposition of the HFA-diolate. These results are in contrast to the photochemical behavior of acetone, butanone and acetaldehyde on TiO2(110), where UV irradiation resulted in the gas phase ejection of one of the carbonyl substituent groups as well as a stoichiometric amount of carboxylate left on the surface. We conclude that fluorination alters the electronic structure of adsorbed carbonyls on TiO2(110) in such a way as to promote complete fragmentation of the adsorbed carbonyl complex to form gas phase CO2 as well as open up additional photodissociation pathways leading to CO production.
2010. "Characterization of Organic Coatings on Hygroscopic Salt Particles and their Atmospheric Impacts." Atmospheric Environment 44(9):1209-1218. doi:10.1016/j.atmosenv.2009.11.047 Abstract The photooxidation of α-pinene in the presence of NO2, with and without added NaNO3 seed particles, has been studied in a large diameter flow tube. Particles formed by homogeneous nucleation and by condensation on the pre-existing seeds were sampled at various stages of the reaction, dried using four diffusion dryers, size selected at different mobility diameters (dm) using a differential mobility analyzer (DMA), and characterized with a single particle mass spectrometer (SPLAT II). It was found that homogeneously nucleated particles are spherical, have a density (ρ) of 1.25 ± 0.02 g cm-3 (± 2 σ) and contain a significant amount of organic nitrates. The mass spectra of the low volatility products condensed on the NaNO3 seed particles were found to be virtually the same as in the case of homogeneous nucleation. The data show that the presence of even a submonolayer of organics on the NaNO3 particles causes water retention that leads to a decrease in particle density and that the amount of water retained increases with organic coating thickness. Thicker coatings appear to inhibit water evaporation from the particle seeds altogether. This suggests that in the atmosphere, where low volatility organics are plentiful, some hygroscopic salts will retain water and have different densities and refractive indices than expected in the absence of the organic coating. This water retention combined with the organic shell on the particles can potentially impact light scattering by these particles and activity as cloud condensation nuclei (CCN), as well as heterogeneous chemistry and photochemistry on the particles.
2010. "In-Situ Characterization of Cloud Condensation Nuclei, Interstitial, and background Particles using Single Particle Mass Spectrometer, SPLAT II." Analytical Chemistry 82(19):7943-7951. doi:10.1021/ac1013892 Abstract Aerosol indirect effect remains the most uncertain aspect of climate change modeling because proper test requires knowledge of individual particles sizes and compositions with high spatial and temporal resolution. We present the first deployment of a single particle mass spectrometer (SPLAT II) that is operated in a dual data acquisition mode to measure all the required individual particle properties with sufficient temporal resolution to definitively resolve the aerosol-cloud interaction in this exemplary case. We measured particle number concentrations, asphericity, and individual particle size, composition, and density with better than 60 seconds resolution. SPLAT II measured particle number concentrations between 70 particles cm-3and 300 particles cm-3, an average particle density of 1.4 g cm-3. Found that most particles are composed of oxygenated organics, many of which are mixed with sulfates. Biomass burn particles some with sulfates were prevalent, particularly at higher altitudes, and processed sea-salt was observed over the ocean. Analysis of cloud residuals shows that with time cloud droplets acquire sulfate by the reaction of peroxide with SO2. Based on the particle mass spectra and densities we find that the compositions of cloud condensation nuclei are similar to those of background aerosol but, contain on average ~7% more sulfate, and do not include dust and metallic particles. A comparison between the size distributions of background, activated, and interstitial particles shows that while nearly none of the activated particles is smaller than 115 nm, more than 80% of interstitial particles are smaller than 115 nm. We conclude that for this cloud the most important difference between CCN and background aerosol is particle size although having more sulfate also helps.
2010. "Effects of Pore-Scale Heterogeneity and Transverse Mixing on Bacterial Growth in Porous Media." Environmental Science & Technology 44(8):3085-3092. Abstract Microbial degradation of contaminants in the subsurface requires the availability of nutrients; this is impacted by porous media heterogeneity and the degree of transverse mixing. Two types of microfluidic pore structures etched into silicon wafers (i.e., micromodels), i) a homogeneous distribution of cylindrical posts and ii) aggregates of large and small cylindrical posts, were used to evaluate the impact of heterogeneity on growth of a pure culture (Delftia acidovorans) that degrades (R)-2-(2,4-dichlorophenoxy)propionate (R-2,4-DP). Following inoculation, dissolved O2 and R-2,4-DP were introduced as two parallel streams that mixed transverse to the direction of flow. In the homogeneous micromodel, biomass growth was uniform in pore bodies along the center mixing line, while in the aggregate micromodel, preferential growth occurred between aggregates and slower less dense growth occurred throughout aggregates along the center mixing line. The homogeneous micromodel had more rapid growth overall (2X), and more R-2,4-DP degradation (9.5%) than the aggregate pore structure (5.7%). Simulation results from a pore-scale reactive transport model indicate mass transfer limitations within aggregates along the center mixing line decreased overall reaction; hence, slower biomass growth rates relative to the homogeneous micromodel are expected. Results from this study contribute to a better understanding of the coupling between mass transfer, reaction rates, and biomass growth in complex porous media, and suggest successful implementation and analysis of bioremediation systems requires knowledge of subsurface heterogeneity.
2010. "Pore-Scale Study of Transverse Mixing Induced CaCO3 Precipitation and Permeability Reduction in a Model Subsurface Sedimentary System." Environmental Science & Technology 44(20):7833-7838. doi:10.1021/es1019788 Abstract A microfluidic pore structure etched into a silicon wafer was used as a two-dimensional model subsurface sedimentary system (i.e., a micromodel) to study mineral precipitation and permeability reduction relevant to groundwater remediation and geological carbon sequestration. Solutions containing CaCl2 and Na2CO3 at four different saturation states ( = [Ca2+] [CO32-] / KspCaCO3) were introduced through two separate inlets and they mixed by diffusion transverse to the main flow direction along the center of the micromodel resulting in CaCO3 precipitation. Precipitation rates increased and the total amount of precipitates decreased with increasing saturation state, and only vaterite and calcite crystals were formed (no aragonite). The relative amount of vaterite increased from 80% at the lowest saturation ( = 2.8 for vaterite) state to 95% at the highest saturation state ( = 4.5). Fluorescent tracer tests conducted before and after CaCO3 precipitation indicate that pore spaces were completely occluded by CaCO3 precipitates along the transverse mixing zone, thus significantly reducing porosity and permeability, and potentially limiting transformation from vaterite to the more stable calcite. The results suggest that mineral precipitation along plume margins can decrease both reactant mixing during groundwater remediation, and injection and storage efficiency during CO2 sequestration.
2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169. Abstract We report a mass spectrometry-based strategy for quantitative analysis of cell surface membrane proteome changes. The strategy includes enrichment of surface membrane proteins using a membrane-impermeable chemical probe followed by stable isotope 18O labeling and LC-MS analysis. We applied this strategy for enriching membrane proteins expressed by Shewanella oneidensis MR-1, a gram-negative bacterium with known metal-reduction capability via extracellular electron transfer between outer membrane proteins and environmental electron receptors. LC/MS/MS analysis resulted in the identification of about 79% membrane proteins among all proteins identified from the enriched sample. To illustrate the quantification of membrane proteome changes, enriched membrane protein samples from wild-type and mutant cells (generated from deletion of a type II secretion protein, GspD) were further labeled with 16O and 18O at the peptide level prior to LC-MS analysis. A chemical-probe-labeled pure protein has also been used as an internal standard for normalization purpose. The quantitative data revealed reduced abundances of many outer membrane proteins such as OmcA and MtrC in ΔgspD mutant cells, which agreed well with previously published studies.
2010. "Nanoscale Phase Transitions under Extreme Conditions within an Ion Track." Journal of Materials Research 25(7):1344-1351. Abstract The dynamics of track development due to the passage of relativistic heavy ions through solids is a long-standing issue relevant to nuclear materials, age-dating of minerals, space exploration, and nanoscale fabrication of novel devices. We have integrated experimental and simulation approaches to investigate nanoscale phase transitions under the extreme conditions created within single tracks of relativistic ions in Gd2O3(TiO2)x and Gd2Zr2-xTixO7. Track size and internal structure depend on energy-density deposition, irradiation temperature, and material composition. Molecular dynamics methods based on the thermal spike model have simulated, for the first time, the internal structure of individual tracks, consistent with experimental observations. Individual ion tracks have nanoscale core-shell structures that provide a unique record of the phase transition pathways under extreme conditions.
2010. "Vapor-Induced Solid-Liquid-Solid Process for Silicon-based Nanowire Growth." Journal of Power Sources 195(6 SP ISS):1691-1697. Abstract Silicon based nanowires have been grown from commercial silicon powders under conditions of differing oxygen and carbon activities. Nanowires grown in the presence of carbon sources consisted of a crystalline SiC core with an amorphous SiOx shell. The thickness of SiOx shell decreased as the oxygen concentration in the precursor gases was lowered. Nanowires grown in a carbon-free environment consisted of amorphous silicon oxide with a typical composition of SiO1.8. The growth rate of nanowires decreased with decreasing oxygen content in the precursor gases. SiO1.8 nanowires exhibited an initial discharge capacity of ~ 1,300 mAh/g and better stability than those of silicon powders. A Vapor Induced Solid-Liquid-Solid (VI-SLS) mechanism is proposed to explain the nanowire growth (including silicon and other metal based nanowires) from powder sources. In this approach, both a gas source and a solid powder source are required for nanowire growth. This mechanism is consistent with experimental observations and can also be used to guide the design and growth of other nanowires.
2010. "Carbon nanotubes decorated with Pt nanoparticles via electrostatic self-assembly: a highly active oxygen reduction electrocatalyst." Journal of Materials Chemistry 20(15):2826-2830. doi:10.1039/b919494k Abstract Carbon nanotubes (CNTs) are noncovalently functionalized with poly(allylamine hydrochloride) (PAH) and then employed as the support of Pt nanoparticles. X-Ray photoelectron spectroscopy confirms the successful functionalization of CNTs with PAH. The negatively charged Pt precursors are adsorbed on positively charged PAH-wrapping CNTs surface via electrostatic self-assembly and then in situ reduced in ethylene glycol. X-Ray diffraction and transmission electron microscope images reveal that Pt nanoparticles with an average size of 2.6 nm are uniformly dispersed on CNT surface. Pt/PAH-CNTs exhibit unexpectedly high activity towards oxygen reduction reaction, which can be attributed to the large electrochemical surface area of Pt nanoparticles. It also shows enhanced electrochemical stability due to the structural integrity of PAH-CNTs. This provides a facile approach to synthesize CNTs-based nanoelectrocatalysts.
2010. "Electrostatic Self-Assembly of Pt-around-Au Nanocomposite with High Activity towards Formic Acid Oxidation." Angewandte Chemie International Edition 49(12):2211-2214. doi:10.1002/anie.200906987 Abstract Pt-around-Au nanocomposite is synthesized using the electrostatic selfassembly method. This catalyst shows significantly improved activity towards formic acid oxidation. The possible reason is the efficient spillover of HCOO from Au to the surrounding Pt NPs, where HCOO is further oxidized to CO2.
2010. "Facile synthesis of PtAu alloy nanoparticles with high activity for formic acid oxidation." Journal of Power Sources 195(4):1103-1106 . doi:10.1016/j.jpowsour.2009.08.054 Abstract We report the facile synthesis of carbon supported PtAu alloy nanoparticles with high electrocatalytic activity as the anode catalyst for direct formic acid fuel cells (DFAFCs). PtAu alloy nanopaticles are synthesized by co-reducing HAuCl4 and H2PtCl6 with NaBH4 in the presence of sodium citrate and then the nanoparticles are deposited on Vulcan XC-72R carbon support (PtAu/C). The obtained catalysts are characterized with X-ray diffraction (XRD) and transmission electron microscope (TEM), which reveal PtAu alloy formation with an average diameter of 4.6 nm. PtAu/C exhibits 8 times higher catalytic activity toward formic acid oxidation than Pt/C. The enhanced activity of PtAu/C catalyst is attributed to noncontinuous Pt sites formed in the presence of the neighbored Au sites, which promotes direct oxidation of formic acid by avoiding poison CO.
2010. "Low-cost and durable catalyst support for fuel cells: graphite submicronparticles." Journal of Power Sources 195(2):457-460. doi:10.1016/j.jpowsour.2009.08.012 Abstract Low-cost graphite submicronparticles (GSP) are employed as a possible catalyst support for polymer electrolyte membrane (PEM) fuel cells. Platinum nanoparticles are deposited on Vulcan XC-72 carbon black (XC-72), carbon nanotubes (CNT), and GSP via ethylene glycol (EG) reduction method. The morphologies and the crystallinity of Pt/XC-72, Pt/CNT, and Pt/GSP are characterized with X-ray diffraction and transmission electron microscope, which shows that Pt nanoparticles (~ 3.5 nm) are uniformly dispersed on GSP support. Pt/GSP exhibits the highest activity towards oxygen reduction reactions. The durability study indicates that Pt/GSP is 2 ~ 3 times durable than Pt/CNT and Pt/XC-72. The enhanced durability of Pt/GSP catalyst is attributed to the higher corrosion resistance of graphite submicronparticles, which results from higher graphitization degree of GSP support. Considering its low production cost, graphite submicronparticles are promising electrocatalyst support for fuel cells.
2010. " Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model ." Journal of Proteome Research 9(3):1496-1509. doi:10.1021/pr901024z Abstract Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration in the nigrostriatal region of the brain; however, the neurodegeneration extends well beyond dopaminergic neurons. To gain a better understanding of the molecular changes relevant to PD, we applied two-dimensional LC-MS/MS to comparatively analyze the proteome changes in four brain regions (striatum, cerebellum, cortex, and the rest of brain) using a MPTP-induced PD mouse model with the objective to identify nigrostriatal-specific and other region-specific protein abundance changes. The combined analyses resulted in the identification of 4,895 non-redundant proteins with at least two unique peptides per protein. The relative abundance changes in each analyzed brain region were estimated based on the spectral count information. A total of 518 proteins were observed with significant MPTP-induced changes across different brain regions. 270 of these proteins were observed with specific changes occurring either only in the striatum and/or in the rest of the brain region that contains substantia nigra, suggesting that these proteins are associated with the underlying nigrostriatal pathways. Many of the proteins that exhibit significant abundance changes were associated with dopamine signaling, mitochondrial dysfunction, the ubiquitin system, calcium signaling, the oxidative stress response, and apoptosis. A set of proteins with either consistent change across all brain regions or with changes specific to the cortex and cerebellum regions were also detected. One of the interesting proteins is ubiquitin specific protease (USP9X), a deubiquination enzyme involved in the protection of proteins from degradation and promotion of the TGF- pathway, which exhibited altered abundances in all brain regions. Western blot validation showed similar spatial changes, suggesting that USP9X is potentially associated with neurodegeneration. Together, this study for the first time presents an overall picture of proteome changes underlying both nigrostriatal pathways and other brain regions potentially involved in MPTP-induced neurodegeneration. The observed molecular changes provide a valuable reference resource for future hypothesis-driven functional studies of PD.
2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9(6):1199-1208. Abstract Oxidative modifications of protein tyrosines have been implicated in multiple human diseases. Among these modifications, elevations in levels of 3, 4-dihydroxyphenylalanine (DOPA), a major product of hydroxyl radical addition to tyrosine, has been observed in a number of pathologies. Here we report the first global proteome survey of endogenous site-specific modifications, i.e, DOPA and its further oxidation product dopaquinone (DQ) in mouse brain and heart tissues. Results from LC-MS/MS analyses included 203 and 71 DOPA-modified tyrosine sites identified from brain and heart, respectively, with a false discovery rate of ~1%; while only a few nitrotyrosine containing peptides, a more commonly studied marker of oxidative stress, were detectable, suggesting the much higher abundance for DOPA modification as compared with tyrosine nitration. Moreover, 57 and 29 DQ modified peptides were observed from brain and heart, respectively; nearly half of these peptides were also observed with DOPA modification on the same sites. For both tissues, these modifications are preferentially found in mitochondrial proteins with metal-binding properties, consistent with metal catalyzed hydroxyl radical formation from mitochondrial superoxide and hydrogen peroxide. These modifications also link to a number of mitochondria-associated and other signaling pathways. Furthermore, many of the modification sites were common sites of previously reported tyrosine phosphorylation suggesting potential disruption of signaling pathways. Structural aspects of DOPA-modified tyrosine sequences are distinct from those of nitrotyrosines suggesting that each type of modifications provides a marker for different in vivo reactive chemistries and can be used to predict sensitive protein targets. Collectively, the results suggest that these modifications are linked with mitochondrially-derived oxidative stress, and may serve as sensitive markers for disease pathologies.
2010. "Damage and Microstructure Evolution in GaN under Au Ion Irradiation." Journal of Physics D. Applied Physics 43(8):085303. doi:10.1088/0022-3727/43/8/085303 Abstract Damage and microstructure evolution in gallium nitride (GaN) under Au+ ion irradiation has been investigated using complementary electron microscopy, secondary ion mass spectrometry and ion beam analysis techniques. Epitaxially-grown GaN layers (2-um-thick) have been irradiated by 2.0 MeV Au ions to 1.0 × 1015 and 1.4 × 1015 cm-2 at 155 K and 7.3 × 1015 cm-2 at 200 K. The irradiation-induced damage has been analyzed by Rutherford backscattering spectroscopy in a channeling direction (RBS/C). For a better determination of ion-induced disorder profile, an iterative procedure and a Monte Carlo code (McChasy) are combined to analyze the ion channeling spectra. With increasing irradiation dose, separated amorphous layers develop from the sample surface and near the damage peak region. Formation of large nitrogen bubbles with sizes up to 70 nm is observed in the buried amorphous layer, while the surface layer contains small bubbles with diameter of a few nanometers due to significant nitrogen loss from the surface. Volume expansion from 3% to 25% in the irradiated region is suggested by cross sectional transmission electron microscope and RBS/C measurement. The anomalous shape of the Au distributions under three irradiations indicates out-diffusion of Au toward sample surface. The results from the complementary techniques suggest that nitrogen is retained in the damaged GaN where the crystallinity is preserved. Once the amorphous state is reached in the surface region, GaN starts to decompose and nitrogen escapes from the surface. Furthermore, experimental results show considerable errors in both disorder profile and ion range predicted by the Stopping and Range of Ions in Matter code, indicating a significant overestimation of electronic stopping powers of Au ions in GaN.
2010. "Damage evolution in Au-implanted Ho2Ti2O7 titanate pyrochlore." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 268(19):3009-3013. doi:10.1016/j.nimb.2010.05.029 Abstract Damage evolution at room temperature in Ho2Ti2O7 single crystals is studied under 1 MeV Au2+ ion irradiation by Rutherford backscattering spectroscopy along the <001> direction. For a better determination of ion-induced disorder profile, an iterative procedure and a Monte Carlo code (McChasy) were used to analyze ion channeling spectra. A disorder accumulation model, with contributions from the amorphous fraction and the crystalline disorder, is fit to the Ho damage accumulation data. The damage evolution behavior indicates that the relative disorder on the Ho sublattice follows a nonlinear dependence on dose and that defect-stimulated amorphization is the primary amorphization mechanism. Similar irradiation behavior previously was observed in Sm2Ti2O7. A slower damage accumulation rate for Ho2Ti2O7, as compared with damage evolution in Sm2Ti2O7, is mainly attributed to a lower effective cross section for defect-simulated amorphization.
2010. "Grain growth and phase stability of nanocrystalline cubic zirconia under ion irradiation." Physical Review. B, Condensed Matter 82(18):184105:1-7. doi:10.1103/PhysRevB.82.184105 Abstract Grain growth, oxygen stoichiometry and phase stability of nanostructurally-stabilized zirconia (NSZ) in pure cubic phase are investigated under 2 MeV Au ion bombardment at 160 and 400 K to doses up to 35 displacements per atom (dpa). The NSZ films are produced by ion-beam-assisted deposition technique at room temperature with an average grain size of 7.7 nm. The grain size increases with dose, and follows a power law (n=6) to a saturation value of ~30 nm that decreases with temperature. Slower grain growth is observed under 400 K irradiations, as compared to 160 K irradiations, indicating that thermal grain growth is not activated and defect-stimulated grain growth is the dominating mechanism. While cubic phase is perfectly retained and no new phases are identified after the high-dose irradiations, reduction of oxygen in the irradiated NSZ films is detected. The ratio of O to Zr decreases from ~2.0 for the as-deposited films to ~1.65 after irradiation to ~35 dpa. Significant increase of oxygen vacancies in nanocrystalline zirconia suggests substantially enhanced oxygen diffusion under ion irradiation, a materials behavior far from equilibrium. The oxygen deficiency may be essential in stabilizing cubic phase to larger grain sizes.
2010. "Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Signal Amplification." Analytical Chemistry 82(15):6440–6446. doi:10.1021/ac1006238 Abstract A novel DNA detection platform based on a hairpin-DNA switch, nanoparticles, and enzyme signal amplification for ultrasensitive detection of DNA hybridization has been developed in this work. In this DNA assay, a “stem-loop” DNA probe dually labeled with a thiol at its 5’ end and a biotin at its 3’ end, respectively, was used. This probe was immobilized on the gold nanoparticles (AuNPs) anchored by a protein, -globulin, on a 96-well microplate. In the absence of target DNA, the immobilized probe with the stem-loop structure shields the biotin from being approached by a bulky horseradish peroxidase linked-avidin (avidin-HRP) conjugate due to the steric hindrance. However, in the presence of target DNA, the hybridization between the hairpin DNA probe and the target DNA causes significant conformational change of the probe, which forces biotin away from the surface of AuNPs. As a result, the biotin becomes accessible by the avidin-HRP, and the target hybridization event can be sensitively detected via the HRP catalyzed substrate 3, 3', 5, 5'-tetramethylbenzidine using spectrophometric method. Some experimental parameters governing the performance of the assay have been optimized. At optimal conditions, this DNA assay can detect DNA at the concentration of femtomolar level by means of a signal amplification strategy based on the combination of enzymes and nanoparticles. This approach also has shown excellent specificity to distinguish single-base mismatches of DNA targets because of the intrinsic high selectivity of the hairpin DNA probe.
2010. "High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D." Acta Crystallographica. Section F 66(12):1610-1613. doi:10.1107/S1744309110039874 Abstract Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level with high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.
2010. "Structural analysis of the receptor binding domain of botulinum neurotoxin serotype D." Biochemical and Biophysical Research Communications 401:498-503. doi:10.1016/j.bbrc.2010.09.063 Abstract Botulinum neurotoxins (BoNTs) are the most toxic proteins known. The mechanism for entry into neuronal cells for serotypes A, B, E, F, and G involves a well understood dual receptor (protein and ganglioside) process, however, the mechanism of entry for serotypes C and D remains unclear. To provide structural insights into how BoNT/D enters neuronal cells, the crystal structure of the receptor binding domain (S863-E1276) for this serotype (BoNT/D-HCR) was determined at 1.65 Å resolution. While BoNT/D-HCR adopts an overall fold similar to that observed in other known BoNT HCRs, several major structural differences are present. These structural differences are located at, or near, putative receptor binding sites and may be responsible for BoNT/D host preferences. Two loops, S1195-I1204 and K1236-N1244, located on both sides of the putative protein receptor binding pocket, are displaced >10 Å relative to the corresponding residues in the crystal structures of BoNT/B and G. Obvious clashes were observed in the putative protein receptor binding site when the BoNT/B protein receptor synaptotagmin II was modeled into the BoNT/D-HCR structure. Although a ganglioside binding site has never been unambiguously identified in BoNT/D-HCR, a shallow cavity in an analogous location to the other BoNT serotypes HCR domains is observed in BoNT/D-HCR that has features compatible with membrane binding. A portion of a loop near the putative receptor binding site, K1236-N1244, is hydrophobic and solvent-exposed and may directly bind membrane lipids. Liposome-binding experiments with BoNT/D-HCR demonstrate that this membrane lipid may be phosphatidylethanolamine.
2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9(11):5698-5704. doi:10.1021/pr100508p Abstract Spectral counting has become a popular semi-quantitative method for LC-MS/MS based proteome quantification; however, this methodology is often not reliable when proteins are identified by a small number of spectra. Here we present a simple strategy to improve spectral counting based quantification for low abundance proteins by recovering low quality or low scoring spectra for confidently identified peptides. In this approach, stringent data filtering criteria were initially applied to achieve confident peptide identifications with low false discovery rate (e.g., <1%) after LC-MS/MS analysis and database search by SEQUEST. Then, all low scoring MS/MS spectra that match to this set of confidently identified peptides were recovered, leading to more than 20% increase of total identified spectra. The validity of these recovered spectra was assessed by the parent ion mass measurement error distribution, retention time distribution, and by comparing the individual low score and high score spectra that correspond to the same peptides. The results support that the recovered low scoring spectra have similar confidence levels in peptide identifications as the spectra passing the initial stringent filter. The application of this strategy of recovering low scoring spectra significantly improved the spectral count quantification statistics for low abundance proteins, as illustrated in the identification of mouse brain region specific proteins.
2010. "Electrochemical Performance and Stability of the Cathode for Solid Oxide Fuel Cells II. Role of Ni diffusion on LSM performance ." Journal of the Electrochemical Society 157(5):B643-B649. Abstract The sintering of a standard (La0.8Sr0.2)0.98MnO3 (LSM-20) solid oxide fuel cell cathode composition (in the temperature range of 1050-1200ºC) on anode-supported cells utilizing a Ni-YSZ anode and thin YSZ electrolyte (<10 m thickness) has revealed the need for a protective ceria interlayer to prevent a detrimental interaction between the YSZ and the LSM. The interaction, however, is not the typically assumed formation of insulating La- and/or Sr-zirconate, but rather the result of Ni diffusion from the anode through the YSZ electrolyte and into the LSM resulting in coarsening and increased densification of the LSM microstructure. As an alternative to the use of a protective ceria interlayer, the presence of YSZ in the cathode material was able to suppress coarsening of LSM, thereby significantly improving the electrochemical performance.
2010. "Electrochemical Performance and Stability of the Cathode for Solid Oxide Fuel Cells: III. Role of volatile boron species on LSM/YSZ and LSCF." Journal of the Electrochemical Society 157(7):B1019-B1023. doi:10.1149/1.3397854 Abstract Boron oxide is a key component to tailor the softening temperature and viscosity of the sealing glass for solid oxide fuel cells. The primary concern regarding the use of boron containing sealing glasses is the volatility of boron species, which possibly results in cathode degradation. In this paper, we report the role of volatile boron species on the electrochemical performance of LSM/YSZ and LSCF cathodes at various SOFC operation temperatures. The transport rate of boron, ~ 3.24×10-12 g/cm2•sec was measured at 750°C with air saturated with 2.8% moisture. A reduction in power density was observed in cells with LSM/YSZ cathodes after introduction of the boron source to the cathode air stream. Partial recovery of the power density was observed after the boron source was removed. Results from post-test secondary ion mass spectroscopy (SIMS) analysis the partial recovery in power density correlated with partil removal of the deposited boron by the clean air stream. The presence of boron was also observed in LSCF cathodes by SIMS analysis, however the effect of boron on the electrochemical performance of LSCF cathode was negligible. Coverage of triple phase boundaries in LSM/YSZ was postulated as the cause for the observed reduction in electrochemical performance.
2010. "Oxygen-induced magnetic properties and metallic behavior of a BN sheet." Journal of Physics. Condensed Matter 22(46):Paper No. 465303. doi:10.1088/0953-8984/22/46/465303 Abstract In this paper, ab initio method has been employed to study the adsorption energies, electronic structures and magnetic properties of a BN sheet functionalized by oxygen (O) atom. The adsorption process is typically exothermic, and some unusual properties can be revealed with different adsorption sites. The energy gap of BN sheet narrows due to the strong hybridization between O and BN electronic states when O locates above a BN bond or a nitrogen atom. Upon the adsorption of O above a B3N3 ring or a boron atom, the electrons of O-adsorbed BN system are polarized, which gives rise to the magnetic moment of 2.0 μB. In this case, Fermi level crosses the valence band, resulting the O-adsorbed BN system to be metallic. Furthermore, potential energy curves analysis shows that the magnetism and matellic of BN system can be modulated by the external temperature and pressure.
2010. "Spin and band-gap engineering in copper-doped BN sheet." Chemical Physics Letters 491(4-6):203-207 . doi:10.1016/j.cplett.2010.03.085 Abstract We perform first-principles calculations on single- or dimer-Cu absorbed BN sheet. It was found that the band gap of BN sheet was reduced due to the emergence of certain impurity states arisen from Cu atom. The value of band gap depends on the adsorption configuration. Unpaired electron in absorbed single-Cu atom is polarized causing a magnetic moment of 1.0 μB, while no magnetic moment has been detected after dimer-Cu adsorption. Comparing the analogous carbon nanostructures, Cu-absorbed BN sheet is more resistant to oxidation and thereby is more experimentally accessible.
2010. "Reactivity of the Gold/Water Interface During Selective Oxidation Catalysis." Science 330(6000):74-78. doi:10.1126/science.1195055 Abstract The selective oxidation of alcohols in aqueous phase over supported metal catalysts is facilitated by high-pH conditions. We have studied the mechanism of ethanol and glycerol oxidation to acids over various supported gold and platinum catalysts. Labeling experiments with 18O₂ and H₂18O demonstrate that oxygen atoms originating from hydroxide ions instead of molecular oxygen are incorporated into the alcohol during the oxidation reaction. Density functional theory calculations suggest that the reaction path involves both solution-mediated and metal-catalyzed elementary steps. Molecular oxygen is proposed to participate in the catalytic cycle not by dissociation to atomic oxygen but by regenerating hydroxide ions formed via the catalytic decomposition of a peroxide intermediate.