Scientific Publications 2010
2010. "Core-Shell Diamond as a Support for Solid-Phase Extraction and High-Performance Liquid Chromatography." Analytical Chemistry 82(11):4448-4456. Abstract We report the formation of core-shell diamond particles for solid phase extraction (SPE) and high performance liquid chromatography (HPLC) made by layer-by-layer (LbL) deposition. Their synthesis begins with the amine functionalization of microdiamond by its immersion in an aqueous solution of a primary amine-containing polymer (polyallylamine (PAAm)). The amine-terminated microdiamond is then immersed in an aqueous suspension of nanodiamond, which leads to adsorption of the nanodiamond. Alternating (self-limiting) immersions in the solutions of the amine-containing polymer and the suspension of nanodiamond are continued until the desired number of nanodiamond layers is formed around the microdiamond. Finally, the core-shell particles are cross-linked with 1,2,5,6-diepoxycyclooctane or reacted with 1,2-epoxyoctadecane. Layer-by-layer deposition of PAAm and nanodiamond is also studied on planar Si/SiO2 surfaces, which were characterized by SEM, Rutherford backscattering spectrometry (RBS) and nuclear reaction analysis (NRA). Core-shell particles are characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), environmental scanning electron microscopy (ESEM), and Brunauer Emmett Teller (BET) surface area and pore size measurements. Larger (ca. 50 μm) core-shell diamond particles have much higher surface areas, and analyte loading capacities in SPE than nonporous solid diamond particles. Smaller (ca. 3 μm), normal and reversed phase, core-shell diamond particles have been used for HPLC, with 36,300 plates per meter for mesitylene in a separation of benzene and alkyl benzenes on a C18 adsorbent, and 54,800 plates per meter for diazinon in a similar separation of two pesticides.
2010. "Chloromethylated activated carbon: A useful new synthon for making a novel class of sorbents for heavy metal separations." Separation Science and Technology 45(2):228-235. doi:10.1080/01496390903423550 Abstract The chloromethylation of activated carbon is described. Chloromethylation was found to produce a carbon derivative with a surface area of 1357 m2/g and no significant change in the pore structure. The product was found to contain ~1.5 mmole of –CH2Cl groups per g of material, similar to the functional density reported in the original Merrifield resin synthesis. Displacement of the benzylic chloride was achieved by treating this material with an excess of sodium thiosulfate in refluxing aqueous methanol. The resulting Bunte salt was then hydrolyzed by treatment with warm 3M HCl to afford the corresponding thiol (“AC-CH2-SH”) cleanly and in high yield. AC-CH2-SH was found to be an effective heavy metal sorbent, efficiently capturing Hg, Pb, Ag and Cu. Sorption kinetics were rapid, with equilibrium achieved in less than 30 minutes
2010. "Thickness Dependency of Thin Film Samaria Doped Ceria for Oxygen Sensing ." IEEE Sensors Journal 11(1):217-224. doi:10.1109/JSEN.2010.2050766 Abstract High temperature oxygen sensors are widely used for exhaust gas monitoring in automobiles. This particular study explores the use of thin film single crystalline samaria doped ceria as the oxygen sensing material. Desired signal to noise ratio can be achieved in a material system with high conductivity. From previous studies it is established that 6 atomic percent samarium doping is the optimum concentration for thin film samaria doped ceria to achieve high ionic conductivity. In this study, the conductivity of the 6 atomic percent samaria doped ceria thin film is measured as a function of the sensing film thickness. Hysteresis and dynamic response of this sensing platform is tested for a range of oxygen pressures from 0.001 Torr to 100 Torr for temperatures above 673 K. An attempt has been made to understand the physics behind the thickness dependent conductivity behavior of this sensing platform by developing a hypothetical operating model and through COMSOL simulations. This study can be used to identify the parameters required to construct a fast, reliable and compact high temperature oxygen sensor.
2010. "Selective Capture of Cesium and Thallium from Natural Waters and Simulated Wastes with Copper Ferrocyanide Functionalized Mesoporous Silica." Journal of Hazardous Materials 182(1-3):225-231. doi:10.1016/j.jhazmat.2010.06.019 Abstract Copper(II) ferrocyanide immobilized inside mesoporous silica MCM-41 supports (Cu-FC-EDA-SAMMSTM) has been evaluated against iron(III) hexacyanoferrate(II) (insoluble Prussian blue) for the sorption of cesium (Cs+) and thallium (Tl+) from natural waters and simulated wastes. The affinities (in term of distribution coefficients, Kd) of both sorbents for Cs and Tl were measured as a function of solution pH, competing cations, and matrices. For the entire pH studied (pH 0.1 to 7.3), Cu-FC-EDA-SAMMS had higher affinities for Cs and Tl (one to two orders of magnitude higher Kd) than Prussian blue and was less negatively impacted by the solution pH, competing cations, and matrices. The adsorption isotherms and kinetics of the two sorbents for Cs and/or Tl were also determined in seawater and simulated acid and alkaline wastes. SAMMS outperformed Prussian blue in terms of maximum adsorption capacity (e.g., 21.7 versus 2.6 mg Cs/g in acid waste stimulant, pH 1.1), and rate (e.g., over 95 wt% of Cs was removed after 2 minutes with SAMMS, while only 75 wt% was removed with Prussian blue). The lower affinity, capacity, and rate of Cs and Tl sorption on Prussian blue than those on Cu-FC-EDA-SAMMS were attributed to the molecular pore sizes, which restrict mass transport, and the insoluble Cs abducts of the Prussian blue, which restrict the ability of neighboring binding sites to further bind Cs ions. On the other hand, the large pores of SAMMS not only enable faster diffusion and faster binding chemistry, but they also allow isolation of binding sites so that one Cs binding event does not impact further Cs binding. In addition, iron (Fe) dissolved from insoluble Prussian blue over 10-fold of that from Cu-FC-EDA-SAMMS after 24 hours of contact time, indicating poorer material stability of Prussian blue.
2010. "The toxicity of lead to Desulfovibrio desulfuricans G20 in the presence of goethite and quartz." Journal of Basic Microbiology 50(2):160-170. doi:10.1002/jobm.200900239 Abstract An aqueous mixture of goethite, quartz, and lead chloride (PbCl2) was treated with the sulfatereducing bacterium, Desulfovibrio desulfuricans G20 (D. desulfuricans G20), in a medium specifically designed to assess metal toxicity. In the presence of 26 μM of soluble Pb, together with the goethite and quartz, D. desulfuricans G20 grew after a lag time of 5 days compared to 2 days in Pb-, goethite-, and quartz-free treatments. In the absence of goethite and quartz, however, with 26 μM soluble Pb, no measurable growth was observed. Results showed that D. desulfuricans G20 first removed Pb from solutions then growth began resulting in black precipitates of Pb and iron sulfides. Transmission electron microscopic analyses of thin sections of D. desulfuricans G20 treated with 10 μM PbCl2 in goethite- and quartz-free treatment showed the presence of a dense deposit of lead sulfide precipitates both in the periplasm and cytoplasm. However, thin sections of D. desulfuricans G20 treated with goethite, quartz, and PbCl2 (26 μM soluble Pb) showed the presence of a dense deposit of iron sulfide precipitates both in the periplasm and cytoplasm. Energy-dispersive X-ray spectroscopy, selected area electron diffraction patterns, or X-ray diffraction analyses confirmed the structure of precipitated Pb inside the cell as galena (PbS) in goethite- and quartz-free treatments, and iron sulfides in treatments with goethite, quartz, and PbCl2. Overall results suggest that even at the same soluble Pb concentration (26 μM), in the presence of goethite and quartz, apparent Pb toxicity to D. desulfuricans G20 decreased significantly. Further, accumulation of lead/iron sulfides inside D. desulfuricans G20 cells depended on the presence of goethite and quartz.
2010. "Bulk Migration of Ni/NiO in Ni-YSZ during Reducing Conditions." Journal of the Electrochemical Society 157(4):B463-B469. doi:10.1149/1.3298442 Abstract Understanding the migration of Ni/NiO in Ni-YSZ can potentially help to design a better solid oxide fuel cell (SOFC) anode. We have observed that extensive hydrogen reduction and methane steam reforming of Ni-YSZ caused bulk migration of Ni/NiO to at least ~ 5 µm deeper from the Ni-YSZ surface. No significant bulk migration effects were detected after simple thermal treatments in non-reducing/non-reforming environment. Surface analysis of a single zirconia grain in the first 10-20 nm region from annealed, hydrogen reduced and methane steam reformed Ni-YSZ shows Ni-enriched surface supporting earlier claims of Ni exsolution. 3D-EBSD analysis of thermally treated sample before exposing it to reducing and reforming environment indicated mixed NiO/YSZ phase with some porosity and random grain orientation. The surface analysis and mapping were carried out using ToF-SIMS and AES whereas EDS maps on FIB sliced areas on Ni-YSZ were utilized for the bulk analysis. The results provide additional information related to complex reactions occurring in SOFC during internal reforming conditions.
2010. "Stabilization of ZnMnO3 Phase from Sol-gel Synthesized Nitrate Precursors ." Journal of Sol-Gel Science and Technology 53(2):141-147. doi:10.1007/s10971-009-2067-2 Abstract The stabilization and analysis of pure ZnMnO3 spinel phase may help to understand the solubility limits of Mn in ZnO in wurtzite and spinel cubic structures. In this report, synthesis and characterization of stable ZnMnO3 phase is discussed which is extracted from sol-gel synthesis of zinc and manganese nitrate precursors. The reflections at higher diffraction angles for this known cubic system with space group Fd3m were calculated with the help of JADE 8.0 program. High resolution X-ray photoelectron spectroscopy measurements of Mn3p position of ZnMnO3 compared with ZnMn2O4 showed a higher binding energy shift ~0.85 eV indicating Mn4+ valence state in ZnMnO3.
2010. "Gas Phase Computational Studies on the Competition Between Nitrile and Water Ligands in Uranyl Complexes." Journal of Physical Chemistry A 114(33):8902-8912. doi:10.1021/jp103227x Abstract The formation of uranyl dicationic complexes containing water and nitrile (acetonitrile, propionitrile, and benzonitrile) ligands, [UO2(H2O)n(RCN)m]2+, has been studied using density functional theory (DFT) with a relativistic effective core potential (RECP) to account for scalar relativistic effects on uranium. It is shown that nitrile addition is favored over the addition of water ligands. Decomposition of these complexes to [UO2OH(H2O)n(RCN)m]+ by the loss of either H3O+ or (RCN+H)+ is also examined. It is found that this reaction occurs when the coordination sphere of uranyl is unsaturated. Additionally, this reaction is influenced by the size of the nitrile ligand with reactions involving acetonitrile being the most prevalent.
2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-. doi:10.1371/journal.pone.0010980 Abstract Abstract Background Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF) would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal. Methods and Principal Findings We applied immunoaffinity separation and high sensitivity and resolution liquid chromatography-mass spectrometry to examine CSF from healthy normal individuals. 2630 proteins in CSF from normal subjects were identified, of which 56% were CSF-specific, not found in the much larger set of 3654 proteins we have identified in plasma. We also examined CSF from groups of subjects who were previously used by other studies as surrogates for normals. They had neurologic symptoms that warranted a lumbar puncture but whose values from the clinical laboratory were reported as normal. We found statistically significant differences between their CSF proteins and our non-neurological normals. We also examined CSF from 10 volunteer subjects who had lumbar punctures at least 4 weeks apart and found that there was little variability in CSF proteins in an individual as compared to subject to subject. Conclusions Our results represent the most comprehensive characterization of true normal CSF to date. This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features.
2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry ." Bioinformatics 26(13):1601-1607. doi:10.1093/bioinformatics/btq245 Abstract Motivation: Ion mobility spectrometry (IMS) has gained significant traction over the past few years as a proven technique for rapid, high-resolution separations of analytes based upon gas-phase ion structure with significant impact in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics techniques such as the elucidation of secondary structure information, identification of post-translational modifications, as well as higher identification rates with reduced experiment times. The high throughput nature of this technique calls for accurate calculation of cross sections, mobilities and associated drift times of peptides, thereby, enabling downstream data analysis. Here we introduce a Support Vector Regression-based model that accurately predicts a peptide’s drift time directly from its amino acid sequence. Results: When tested on an experimentally created high confidence database of 8676 peptide sequences with measured drift times, our prediction method statistically significantly outperforms the intrinsic size parameters-based calculations on all charge states (+2,+3 and +4). Availability: The software executable, imPredict, is available for download from http://omics.pnl.gov/software/imPredict.php.
2010. "In-Situ Measurements of Engineered Nanoporous Particle Transport in Saturated Porous Media." Environmental Science & Technology 44(21):8190-8195. doi:10.1021/es1015586 Abstract Engineered nanoporous particles have become an important class of nano-structured materials that have found their increasing industrial, energy, and environmental applications. The internal pore surfaces in the particles can be chemically tailored to sequestrate metals and radionuclide contaminants from groundwater. The fate and transport of the nanoporous particles in subsurface environments, however, have not been studied. Here we present a scanning optical fiber fluorescence profiler that can be used to in situ measure the transport of fluorescence-tagged colloidal and nano-structured particles in column systems. Engineered nanoporous silicate particles (ENSPs) that were covalently bonded with fluorescence-emitting, and uranium-chelating ligands in the intraparticle pore domains were synthesized and used as an example to investigate the nanoporous particle transport and to demonstrate the application of the developed in situ measurement profiler. The profiler detected an irreversible or slowly detached fraction of ENSPs in the sand collector even under conditions thermodynamically unfavorable to particle attachment. Further, the in situ measurement system detected the spatial variability of ENSPs transport that deviated from one-dimensional, homogeneous assumption that is typically used to model particle transport in the column. Generally, however, both measured and model-calculated results indicated that the transport of ENSPs were consistent with that of nonporous colloidal particles that subjected to coupled reversible attachment/detachment and straining processes. The developed system can also be applied to detect other fluorescence-tagged nano-structured or colloidal particle transport.
2010. "Facile and controllable electrochemical reduction of graphene oxide and its applications." Journal of Materials Chemistry 20(4):743-748. Abstract Graphene oxide is electrochemically reduced which is called electrochemically reduced graphene oxide (ER-G). ER-G is characterized with scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The oxygen content is significantly decreased and the sp 2 carbon is restored after electrochemical reduction. ER-G exhibits much higher electrochemical capacitance and cycling durability than carbon nanotubes (CNTs) and chemically reduced graphene; the specific capacitance measured with cyclic voltammetry (20 mV/s) is ~165 F/g, ~86 F/g, and ~100 F/g for ER-G, CNTs, and chemically reduced graphene,1 respectively. The electrochemical reduction of oxygen and hydrogen peroxide was greatly enhanced on ER-G electrodes as compared with CNTs. ER-G has shown a good potential for applications in energy storage, biosensors, and electrocatalysis.
2010. "Highly durable graphene nanoplatelets supported Pt nanocatalysts for oxygen reduction ." Journal of Power Sources 195(15):4600-4605. Abstract We report graphene nanoplatelets (GNP), which exhibit the advantages of both single-layer graphene and highly graphitic carbon, as a durable alternative support material for Pt nanoparticles for oxygen reduction in fuel cells. Pt nanoparticles are deposited on poly(diallyldimethylammonium chloride)(PDDA)-coated GNP, and characterized with transmission electron microscopy, X-ray diffraction, Raman spectra, and electrochemical tests. Pt/GNP exhibits greatly enhanced electrochemical durability (2-3 times that of Pt/CNT and commercial Etek Pt/C). These are attributed to the intrinsic high graphitization degree of GNP and the enhanced Pt-carbon interaction in Pt/GNP. If considering that GNP can be easily mass produced from graphite, GNP is a promising, low-cost, and durable electrocatalyst support for oxygen reduction in fuel cells.
2010. "Nitrogen-doped Graphene and Its Electrochemical Applications." Journal of Materials Chemistry 20(35):7491-7496. doi:10.1039/c0jm00782j Abstract Nitrogen-doped graphene (N-graphene) is obtained by exposing graphene to nitrogen plasma. N-graphene exhibits much higher electrocatalytic activity toward oxygen reduction and H2O2 reduction than graphene, and much higher durability and selectivity than the widely-used expensive Pt. The excellent electrochemical performance of N-graphene is attributed to nitrogen functional groups and the specific properties of graphene. This indicates that N-graphene is promising for applications in electrochemical energy devices (fuel cells, metal-air batteries) and biosensors.
2010. "Noncovalently functionalized graphitic mesoporous carbon as a stable support of Pt nanoparticles for oxygen reduction." Journal of Power Sources 195(7 SP ISS):1805-1811. Abstract We report the facile synthesis of an extremely durable electrocatalyst for oxygen reduction with highly graphitized mesoporous carbon (GMPC) as support (Pt/GMPC). GMPC is prepared through graphitizing the self-assembled soft-template mesoporous carbon (MPC) under high temperature. Most of the mesoporous structures and the specific surface area of MPC are retained even after 2800 °C heat-treatment, and the graphitization degree is greatly improved. GMPC is then noncovalently functionalized with poly(diallyldimethylammonium chloride) (PDDA) and then coated with Pt nanoparticles with ethylene glycol reduction method. Pt nanoparticles of ~3.0 nm in diameter are uniformly dispersed on GMPC. Pt/GMPC exhibits a higher activity towards oxygen reduction reaction (ORR) than Pt nanoparticles supported on Vulcan XC-72 carbon (Pt/XC-72). The durability of Pt/GMPC is improved by a factor of ~2 compared with Pt/XC-72. The enhanced activity and durability of Pt/GMPC are attributed to the graphitic structure of GMPC which makes GMPC more resistant to corrosion and the interaction between Pt nanoparticles and GMPC stronger. GMPC is promising as catalyst support. This provides a facile, eco-friendly promising strategy, avoiding the usually used chemical functionalization of carbon support with oxidizing strong acid, to synthesize electrocatalysts with high durability and activity for polymer electrolyte membrane fuel cells. This strategy can be widely applied in synthesizing metal nanoparticles on hydrophobic support materials.
2010. "Solid-State Hydriding Mechanism in the LiBH4 + MgH2 System." Journal of Physical Chemistry C 114(17):8089-8098. doi:10.1021/jp1003837 Abstract The LiBH4+MgH2 system has great potential in reversible hydrogen storage for fuel cell vehicles. However, it has always been dehydrogenated and re-hydrogenated in the liquid state until recently. The solid-state hydriding and dehydriding are necessary in order to achieve hydrogen uptake and release near the ambient temperature. In this study, the solid-state hydriding mechanism of 2LiH+MgB2 mixtures has been investigated for the first time. It is found that the solid-state hydriding proceeds in two elementary steps. The first step is the ion exchange between the Mg2+ and Li+ ions in the MgB2 crystal to form an intermediate compound (Mg1-xLi2x)B2. The second step is the continuous ion exchange and simultaneous hydrogenation of (Mg1-xLi2x)B2 to form LiBH4 and MgH2. This finding is consistent with the observed diffusion-controlled hydriding kinetics.*
2010. "Characterization of a New Phase of Ammonia Borane." Energy & Environmental Science 3(6):796-804. Abstract An uncharacterized phase of ammonia borane (AB) was previously identified while investigating its thermal decomposition. This phase was identified as a key intermediate for the release of hydrogen from AB prompting the current characterization study. The new phase was investigated extensively using in situ solid state MAS NMR spectroscopy, including 11B, 15N and 1H NMR. Single-pulse excitation, cross polarization and T1 relaxation experiments collectively demonstrate a significant increase in mobility for the new phase when compared to the room temperature crystalline phase of AB. However, the data are not completely consistent with a liquid phase. The data are also not consistent with a solid phase, but are most consistent with a phase best described as “liquid-like”. This implies a disruption of the long-range order which is primarily stabilized by the extensive dihydrogen bonding network, allowing increased motional freedom. X-ray diffraction and Raman thermal decomposition data of neat AB provide support for a disordered phase, as does data of AB immobilized into a mesoporous scaffold. These observations suggest that a breakdown of the extensive hydrogen bonding network is necessary before hydrogen can be released and will be an important factor in the practical use of AB as a hydrogen storage material. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133. doi:10.1371/journal.pone.0013133 Abstract We report on the degradomic-peptidomic insights into blood plasma of early-stage breast cancer patients. The plasmin-2-antiplasmin and thrombin-antithrombin systems are observed to be changed in early stage breast cancer through the selective degradation of their functional domains. The extracellular matrix (ECM) protection protein complexes are destroyed, but the ECM itself is not massively degraded. Key innate immune system components and cancer inhibitor and suppressor substrates are differentially degraded. The degradomic-peptidomic analysis provides information on the selectivity and extent of substrate and functional domain degradation and the specificity of substrate cleavages, potentially enabling discovery of diagnostic and therapeutic targets for early-stage breast cancer.
2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346. doi:10.1021/pr901083m Abstract Human degradome and its peptidome products are closely related with many pathologic states including cancer. Detection of the peptidome products can provide information of the protein degradation and the activity of the intercellular and intracellular proteases related to diseases. In this work, we describe the AC/SEC-HRLC-FT MS/MS-UStags strategy for top-down analysis of the human blood peptidome components and their modifications. The human blood peptidome is isolated through application of AC/SEC, which enriches its components by >300-fold. These components are separated by the long column HRLC providing a peak capacity of ~300 for the components having MW of up to 20 kDa under the condition of elongated elution. The separated species are identified by the FT MS/MS-UStags sequencing method. From the examined blood plasma sampled from a healthy person, we identified >200 peptidome peptides that originated from 29 degradome substrates from the IPI human protein database (~70,000 entries) without the identification errors. The peptidome peptide sequence mutations and modifications, including acetylation, cysteinylation, acetylhexosamine, oxidation, didehydro, amidation, and pyro-glu, were observed for the peptidome components. Intact low molecular weight proteins were observed only having modified forms. The strategy described here is now used to study the degradation activities in the early-stage breast cancer patient blood, including the selectivity for degradome substrates and functional domains, the peptide cleavage specificity, and the magnitude of degradome substrate involvements in degradation, which provides the insights and footprints for the disease-related degradations in the blood.
2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9(8):4053-4060. Abstract Disulfide bonds are a form of posttranslational modification that often determines protein structure(s) and function(s). In this work, we report a mass spectrometry method for identification of disulfides in degradation products of proteins, and specifically endogenous peptides in the human blood plasma peptidome. LC-Fourier transform tandem mass spectrometry (FT MS/MS) was used for acquiring mass spectra that were de novo sequenced and then searched against the IPI human protein database. Through the use of unique sequence tags (UStags) we unambiguously correlated the spectra to specific database proteins. Examination of the UStags’ prefix and/or suffix sequences that contain cysteine(s) in conjunction with sequences of the UStags-specified database proteins is shown to enable the unambigious determination of disulfide bonds. Using this method, we identified the intermolecular and intramolecular disulfides in human blood plasma peptidome peptides that have molecular weights of up to ~10 kDa.
2010. "Preparation of homogeneous gold-silver alloy nanoparticles using the apoferritin cavity as a nanoreactor." Journal of Physical Chemistry C 114(13):5985-5989. doi:10.1021/jp911004a Abstract Homogeneous Au-Ag alloy nanoparticles have been synthesized in the cavity of horse spleen apoferritin (HSAF) by a diffusion technique. Low concentration of NH4OH solution has been used stabilize Ag(I) ions at pH 8.3, where channels between the subunits of HASF are open for the diffusion of metal ions. The Au-Ag nanoparticle cores are 5.6-6.3 nm in diameter with narrow size distribution (≤ 1.0 nm), and their average diameter was gradually increased with an increase of Ag content. The core formation ratios of Au-Ag-HASF samples are higher than 80%. These series of nanoparticles were applied for the reduction of 4-nitrophenol in the presence of NaBH4. As the Au content was increased in the Au-Ag-HSAF nanoparticles, the rate constant of the reduction was exponentially increased from 1.3 x 10-3 s-1 (pure Ag-HSAF) to 7.58 x 10-2 s-1 (pure Au-HSAF). These synthesized Au-Ag nanoparticles with different compositions will be further applicable in catalysis, sensing, and biomedical areas.
2010. "Differential Ion Mobility Separations of Peptides with Resolving Power Exceeding 50." Analytical Chemistry 82(1):32-35. doi:10.1021/ac902133n Abstract Differential ion mobility spectrometry (IMS) or field asymmetric waveform IMS (FAIMS) sorts gas-phase ions by mobility differences with respect to the electric field intensity. A major emerging FAIMS application is the fractionation of proteolytic digests. Using a planar FAIMS unit with helium/nitrogen mixtures, we have increased FAIMS resolving powers for peptide analyses from the prior maximum of ~20 - 30 to ~50 - 70. The resolution improved nearly 3-fold, allowing, in particular, separation of previously unresolved conformers.
2010. "High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields." Analytical Chemistry 82(18):7649-7655. doi:10.1021/ac101413k Abstract Analyses of complex or isomeric mixtures increasingly involve ion mobility spectrometry/ mass spectrometry (IMS/MS). The IMS methods are grouped into conventional, based on the absolute ion mobility, and differential or field asymmetric waveform IMS (FAIMS), based on the mobility difference in strong and weak electric fields. The key attraction of FAIMS is substantial orthogonality to MS, and several FAIMS/MS platforms have been commercialized. However, the utility of FAIMS had been constrained by limited resolving power, typically R ~ 10 - 20. Recently, the use of helium/nitrogen mixtures comprising up to 75% He has enabled R > 100, with broad resolution gains allowing separation of previously “co-eluting” isomers. These performance metrics open major new FAIMS applications in proteomic and other biological analyses. Here, we show that raising the separation field by ~35% over the previous 21 kV/cm provides similar or better resolution at 50% He, while avoiding problems due to elevated gas pressure in the MS manifold upon excessive He intake. In particular, a resolving power of >200 has been achieved for multiply-charged peptides. The field heating of ions under these conditions appears to exceed that at higher He content but weaker separation field, inducing greater izomerization of fragile species.
2010. "High-Resolution Differential Ion Mobility Separations Using Helium-Rich Gases." Analytical Chemistry 82(6):2456-2462. Abstract Analyses of complex mixtures and characterization of ions increasingly involve gas-phase separations by ion mobility spectrometry (IMS), and particularly differential or field asymmetric waveform IMS (FAIMS) that operates based on the difference of ion mobility in strong and weak electric fields. The key advantage of FAIMS is substantial orthogonality to mass spectrometry (MS), which makes FAIMS/MS hybrid a powerful analytical platform of broad utility. However, the potential of FAIMS has been constrained by limited resolution. Here we report that the use of gas mixtures comprising up to 75% helium dramatically increases the FAIMS separation capability, with the resolving power for peptides and peak capacity for protein digests reaching and exceeding 100. The resolution gains extend to small molecules, where previously unresolved isomers can now be separated. These performance levels open major new applications of FAIMS in proteomic and other biomolecular analyses.
2010. "Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry ." Analytical Chemistry 82(19):8047-8051. doi:10.1021/ac101992d Abstract Since early 1900-s, when vacuum techniques and ion detectors first enabled investigations of gas-phase ions, two approaches to their separation and characterization have emerged - mass spectrometry (MS) and ion mobility spectrometry (IMS).1,2 Though both exploit that distinct charged species move in electric fields differently, MS is performed in vacuum and is based only on the ion mass/charge (m/q) ratio while IMS involves sufficiently dense buffer gases and relies on ion transport properties. The first major discovery enabled by MS was the existence of isotopes by Thomson and Aston,3 and isotopic analyses have since been integral to MS. In particular, the preparative separation of U isotopes using Lawrence’s Calutron was the first industrial application of MS,4 and isotopic labeling is key to MS quantification methods. With IMS, the issue of isotopes was largely ignored as the resolving power (R) was generally too low for their separation. Here, we demonstrate that recently developed high-resolution differential IMS can separate isotopic molecular ions, including nominal isobars with different isotopic content and isotopomers. This capability may enable a new method for isotope separation in a small-scale format at ambient pressure and aid localization of labeled sites in various molecules. Perhaps most importantly, the isotopic shifts depend on the labeled atom position and thus may contain the kind of detailed structural information that is available in solution or solid state using tools such as NMR but has not generally been obtainable for gas-phase ions.
2010. "Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry." Analytical Chemistry 82(19):8327-8334. doi:10.1021/ac101878a Abstract Many proteins and proteolytic peptides incorporate the same post-translational modification (PTM) at different sites, creating multiple localization variants with different functions or activities that may coexist in cells. Current analytical methods based on liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS) are challenged by such isomers that often co-elute in LC and/or produce non-unique fragments. Application of ion mobility spectrometry (IMS) has previously been explored, but success was limited by insufficient resolution. We show that the recently developed high-resolution differential ion mobility spectrometry (FAIMS) using helium-rich gases can readily separate phosphopeptides with variant modified sites. Specifically, use of He/N2 mixtures containing up to 74% He has allowed separating to >95% three monophosphorylated peptides of identical sequence. Similar separation was achieved at 50% He, using an elevated electric field. Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate the FAIMS capabilities for such separations to extend to other PTMs.
2010. "Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection." Proteomics - Clinical Applications 4(1):32-47. doi:10.1002/prca.200900124 Abstract Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. We used shotgun proteomics using LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls (HC). A total of 1446 urinary proteins were identified along with a number of NS specific, renal transplantation specific and AR specific proteins. Relative abundance of identified urinary proteins was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific urinary proteins in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (UMOD, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these urinary proteins in AR. This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of urinary proteins for serial, non-invasive clinical monitoring for graft rejection after
2010. "Structure, Charge Distribution, and Electron Hopping Dynamics in Magnetite (Fe3O4) (100) Surfaces from First Principles." Geochimica et Cosmochimica Acta 74(15):4234-4248. Abstract For the purpose of improving fundamental understanding of the redox reactivity of magnetite, quantum mechanical calculations were applied to predict Fe2+ availability and electron hopping rates at magnetite (100) surfaces, with and without the presence of adsorbed water. Using a low free energy surface reconstruction (½ Fetet layer relaxed into the Feoct (100) plane), the relaxed outermost layer of both the hydrated and vacuum-terminated surfaces were found to be predominantly enriched in Fe2+ within the octahedral sublattice, irrespective of the presence of adsorbed water. At room temperature, mobile electrons move through the octahedral sublattice by Fe2+-Fe3+ valence interchange small polaron hopping, calculated at 1010-1012 hops/second for bulk and bulk-like (i.e. near-surface) environments. This process is envisioned to control sustainable overall rates of interfacial redox reactions. These rates decrease by up to three orders of magnitude (109 hops/second) at the (100) surface, and no significant difference is observed for vacuum-terminated versus hydrated cases. Slower hopping rates at the surface appear to arise primarily from larger reorganization energies associated with octahedral Fe2+-Fe3+ valence interchange in relaxed surface configurations, and secondarily on local charge distribution patterns surrounding Fe2+-Fe3+ valence interchange pairs. These results suggest that, with respect to the possibility that the rate and extent of surface redox reactions depend on Fe2+ availability and its replenishment rate, bulk electron hopping mobility is an upper-limit for magnetite and slower surface rates may need to be considered as potentially rate-limiting. They also suggest hopping mobilities in magnetite nanoparticles may be slower than for bulk single crystals, towards time-scales amenable to Fe2+-Fe3+ site discrimination by conventional spectroscopic probes.
2010. "Technetium incorporation into hematite (α-Fe2O3)." Environmental Science & Technology 44(15):5855-5861 . Abstract Quantum-mechanical methods were used to evaluate mechanisms for possible structural incorporation of Tc species into the model iron oxide, hematite (α-Fe2O3). Using periodic supercell models, energies for charge-neutral incorporation of Tc4+ or TcO4 ions were calculated using either a Tc4+/Fe2+ substitution scheme on the metal sublattice, or by insertion of TcO4 as an interstitial species within a hypothetical vacancy cluster. Although pertechnetate incorporation is found to be invariably unfavorable, incorporation of small amounts of Tc4+ (at least 2.6 wt %) is energetically feasible. Energy minimized bond distances around this impurity are provided to aid in future spectroscopic identification of these impurity species. The calculations also show that Fe2+ and Tc4+ prefer to cluster in the hematite lattice, likely due to less net Coulombic repulsion relative to that of Fe3+-Fe3+. These modeling predictions are generally consistent with observed selective association of Tc with iron oxide under reducing conditions, and in residual waste solids from underground storage tanks at the U.S. Department of Energy Hanford Site (Washington, U.S.A.). Here, even though relatively high pH and oxidizing conditions are dominant, Tc incorporation into iron oxides and (oxy)hydroxides is prospectively enabled by prior reduction of TcO4 to Tc4+ due to interaction with radiolytic species.
2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5(5):Article Number: e10487. Abstract Abstract Background: Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Methodology/Principal Findings: Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. Conclusions/Significance: We propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. We propose a model in which the RNA-binding activity of cspE and cspL selectively enables protein synthesis of the iron acquisition protein sfuC during transient growth-limiting episodes of iron scarcity.
2010. "Breaking through the Glass Ceiling: The Correlation Between the Self-Diffusivity in and Krypton Permeation through Deeply Supercooled Liquid Nanoscale Methanol Films." Journal of Chemical Physics 132(12):Art. No. 124502. doi:10.1063/1.3361664 Abstract Molecular beam techniques, temperature-programmed desorption (TPD), and reflection absorption infrared spectroscopy (RAIRS) are used to explore the relationship between krypton permeation through and the self-diffusivity of supercooled liquid methanol at temperatures near (100-115 K) the glass transition temperature, Tg (103 K). Layered films, consisting of CH3OH and CD3OH, are deposited ontop of a monolayer of Kr on a graphene covered Pt(111) substrate at 25 K. Concurrent Kr TPD and RAIRS spectra are acquired during the heating of the composite film to temperatures above Tg. The CO vibrational stretch is sensitive to the local molecular environment and is used to determine the supercooled liquid diffusivity from the intermixing of the isotopic layers. We find that the Kr permeation and the diffusivity of the supercooled liquid are directly and quantitatively correlated. These results validate the rare gas permeation technique as a tool for probing the diffusivity of supercooled liquids.
2010. "Measuring Diffusivity in Supercooled Liquid Nanoscale Films using Inert Gas Permeation: I. Kinetic Model and Scaling Methods." Journal of Chemical Physics 133(17):174504-11. doi:10.1063/1.3497654 Abstract We describe in detail a diffusion model used to simulate inert gas transport through supercooled liquid overlayers. In recent work, the transport of the inert gas has been shown to be an effective probe of the diffusivity of supercooled liquid methanol in the experimentally challenging regime near the glass transition temperature. The model simulations accurately and quantitatively describe the inert gas permeation desorption spectra. The simulation results are used to validate universal scaling relationships between the diffusivity, overlayer thickness, and the temperature ramp rate for isothermal and temperature programmed desorption. From these scaling relationships we derive simple equations from which the diffusivity can be obtained using the peak desorption time or temperature for an isothermal or set of TPD experiments respectively without numerical simulation. The results presented here demonstrate that the permeation of gases through amorphous overlayers has the potential to be a powerful technique to obtain diffusivity data in deeply supercooled liquids.
2010. "Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions." Journal of Molecular Graphics and Modelling 28(8):755-765. doi:10.1016/j.jmgm.2010.01.013 Abstract The development of stable scaffolds that can tolerate environmental extremes has an immense potential for applications in industry and defense. Recently, we have engineered an eight-residue loop into the de novo designed Top7 protein, which specifically binds the glycoprotein CD4. The robust properties of the Top7, coupled with the ease in production, make it a robust scaffold to design novel functionalities for use under extreme environmental conditions. In the present work, a series of explicit-solvent molecular dynamics simulations are reported which investigates the effect of mutations and extreme conditions of temperature and pH on the structure, stability, and dynamics of the native and engineered Top7. These simulations indicate that i. The structural dynamics of the engineered and native Top7 in solution are equivalent under corresponding conditions of pH and temperature. Ensemble-averaged structures of the native and engineered Top7 maintain the overall tertiary structure pattern, albeit with loss of helical content when at low pH and high-temperature conditions. Mutations of residues E43A, D46A, E67A, E69A, EA81A along the ?-helices of the engineered Top7 did not lead to significant changes in the native fold under pH 2 and 400 K, suggesting that the helices can accommodate varying sequences. iii. The anti-parallel ?-sheet is the structural core responsible for the stability of the native and engineered Top7 and is well maintained under extreme pH and temperature conditions. These findings indicate that the insertion of an eight-residue loop into the structure of Top7 does not adversely affect the global fold or the structural stability of the Top7 scaffold.
2010. "Perturbations in the Lipid Profile of Individuals with Newly Diagnosed Type 1 Diabetes Mellitus: Lipidomics Analysis of a Diabetes Antibody Standardization Program Sample Subset." Clinical Biochemistry 43(12):948-956. Abstract Objectives: To characterize the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus using LC-MS-based lipidomics and the accurate mass and time (AMT) tag approach. Design and methods: Lipids were extracted from plasma and sera of 10 subjects from the Diabetes Antibody Standardization Program (years 2000-2005) and 10 non-diabetic subjects and analyzed by capillary liquid chromatography coupled with a hybrid ion-trap-Fourier transform ion cyclotron resonance mass spectrometer. Lipids were identified and quantified using the AMT tag approach. Results: Five hundred sixty lipid features differentiated (q < 0.05) diabetic from healthy individuals in a partial least-squares analysis, characterizing of individuals with recently diagnosed type 1 diabetes mellitus. Conclusions: A lipid profile associated with newly diagnosed type 1 diabetes may aid in further characterization of biochemical pathways involved in lipid regulation or mobilization and lipotoxicity of pancreatic beta-cells.
2010. "High Resolution NMR Spectroscopy of Nanocrystalline Proteins at Ultra-High Magnetic Field." Journal of Biomolecular NMR 46(2):149-155. doi:10.1007/s10858-009-9389-9 Abstract Solid-state NMR (SSNMR) spectroscopy is a powerful tool for studying protein structure and function, uniquely able to address macroscopically disordered proteins. Insights from SSNMR include atomic-resolution structure, site-specific dynamics, metal center chemistry, and orientation of membrane proteins in bilayers.
2010. "Lattice-Strain Control of the Activity in Dealloyed Core-Shell Fuel Cell Catalysts." Nature Chemistry 2(6):454-460. doi:10.1038/nchem.623 Abstract Electrocatalysis will play a key role in future energy conversion and storage technologies, such as water electrolysers, fuel cells and metal–air batteries. Molecular interactions between chemical reactants and the catalytic surface control the activity and efficiency, and hence need to be optimized; however, generalized experimental strategies to do so are scarce. Here we show how lattice strain can be used experimentally to tune the catalytic activity of dealloyed bimetallic nanoparticles for the oxygen-reduction reaction, a key barrier to the application of fuel cells and metal–air batteries. We demonstrate the core–shell structure of the catalyst and clarify the mechanistic origin of its activity. The platinum-rich shell exhibits compressive strain, which results in a shift of the electronic band structure of platinum and weakening chemisorption of oxygenated species. We combine synthesis, measurements and an understanding of strain from theory to generate a reactivity–strain relationship that provides guidelines for tuning electrocatalytic activity.
2010. "The Role of Non-Covalent Interactions in Electrocatalytic Fuel-Cell Reactions on Platinum." Nature Chemistry 1(6):466-472. doi:10.1038/nchem.330 Abstract The classic models of metal electrode–electrolyte interfaces generally focus on either covalent interactions between adsorbates and solid surfaces or on long-range electrolyte–metal electrostatic interactions. Here we demonstrate that these traditional models are insufficient. To understand electrocatalytic trends in the oxygen reduction reaction (ORR), the hydrogen oxidation reaction (HOR) and the oxidation of methanol on platinum surfaces in alkaline electrolytes, noncovalent interactions must be considered. We find that non-covalent interactions between hydrated alkali metal cations M⁺(H2O)x and adsorbed OH (OHad) species increase in the same order as the hydration energies of the corresponding cations (Li⁺>> Na⁺> K⁺> Cs⁺) and also correspond to an increase in the concentration of OHad–M⁺ (H2O)x clusters at the interface. These trends are inversely proportional to the activities of the ORR, the HOR and the oxidation of methanol on platinum (Cs⁺> K⁺> Na⁺>> Li⁺), which suggests that the clusters block the platinum active sites for electrocatalytic reactions. interface. These trends are inversely proportional to the activities of the ORR, the HOR and the oxidation of methanol on platinum (Cs+> K+> Na+>> Li+), which suggests that the clusters block the platinum active sites for electrocatalytic reactions.
2010. "Impact of Particle Generation Method on the Apparent Hygroscopicity of Insoluble Mineral Particles." Aerosol Science and Technology 44(10):830-846. doi:10.1080/02786826.2010.497514 Abstract Atmospheric mineral dust particles represent a major component of tropospheric aerosol mass and provide a reactive surface for heterogeneous reactions with trace atmospheric gases (Dentener et al. 1996).Heterogeneous processes alter the chemical balance of the atmosphere and also modify the physicochemical properties of mineral dust particles (Bauer et al. 2004). Organic and inorganic vapors can react with or partition to dust particles and alter their chemical composition (Al-Hosney et al. 2005; Laskin et al. 2005a, 2005b; Liu et al. 2008; Sullivan et al. 2007, 2009a; Sullivan and Prather 2007; Usher et al. 2003). Calcite (CaCO3) is one of the most reactive components of mineral dust, readily reacting with acidic gases. The fraction of CaCO3 in total dust mineralogy displays large variations between desert regions and other regions of the world as well as between individual mineral particles (Claquin et al. 1999; Jeong 2008; Laskin et al. 2005b; Sullivan et al. 2007). Through reactions with acidic gases CaCO3 can be converted to soluble hygroscopic products including CaCl2 and Ca(NO3)2, and sparingly soluble, non-hygroscopic products including CaSO4 and CaC2O4 (Krueger et al. 2004; Liu et al. 2008; Sullivan et al. 2009a, 2009b).
2010. "Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry using Poly(dimethylsiloxane) Microchips with Monolithically Integrated Emitters." Analyst 135(9):2296-2302. Abstract Poly(dimethylsiloxane) (PDMS) is the most widely used substrate for microfluidic devices as it enables facile fabrication and has other distinctive properties. However, for applications involving highly sensitive nanoelectrospray ionization mass spectrometry (nanoESI-MS) detection, the use of PDMS microdevices has been hindered by the leaching of uncross-linked oligomers and other contaminants from the substrate that yields a large background of chemical noise in the mass spectra. A more general challenge is that microfluidic devices containing integrated electrospray emitters are frequently unable to operate stably in the nanoflow regime where the best sensitivity is achieved. In this report, we extracted the contaminants from PDMS substrates using a series of solvents, eliminating the background observed when untreated PDMS microchips are used for nanoESI-MS. Optimization of the integrated emitter geometry enabled stable operation at flow rates as low as 10 nL/min. Peptide concentrations of 1 nM were readily detected, representing ~170 zmol of consumed analyte, and an extrapolated detection limit of ~40 zmol; these are the lowest mass and concentration detection limits reported to date for a microchip having an integrated electrospray emitter.
2010. "Photoluminescence Properties of Alkaline-Earth Oxide Nanoparticles." ECS Transactions 28(3):67-80. doi:10.1149/1.3367212 Abstract Previous experiments have demonstrated that photoluminescence properties, both excitation and emission spectra, of powdered MgO depend strongly on the powder preparation and treatment. Similar dependencies have been found for CaO, SrO, and BaO powders. The observed broad photoemission bands have been attributed to the low-coordinated surface sites. Recent advances in nanoscale science and technology have made it possible to produce nearly monodispersed alkaline-earth oxide nanoparticles of very high surface area and investigate their optical properties in details. Here we present the results of our theoretical and experimental work in this area and present new results.
2010. "Analysis of Fe Nanoparticles Using XPS Measurements Under D.C. or Pulsed-Voltage Bias." Surface and Interface Analysis 42(6-7):859-862. doi:10.1002/sia.3260 Abstract The impact of solution exposure on the charging properties of oxide coatings on Fe metal-core oxide-shells has been examined by sample biasing during XPS measurements. The Fe nanoparticles were suspended in relatively unreactive acetone and were analyzed after particle containing solutions were deposited on SiO2/Si substrates, and/or Au substrates. The particle and substrate combinations were subjected to ± 10V d.c. biasing in the form of square waves (SQW) pulses with 5V amplitude. The samples experienced variable degrees of charging for which low energy electrons at ~1 eV, 20μA and low energy Ar+ ions were used to minimize. Application of d.c. bias and/or square wave pulses drastically influences the extent of charging, which is utilized to gather additional analytical information about the sample under investigation. This approach allows separation of otherwise overlapping peaks. Accordingly, the O1s peaks of the silicon oxide substrate, the iron oxide nanoparticles, and that of the casting solvent can be separated from each other. Similarly the C1s peak belonging to the solvent can be separated from that of the adventitious carbon. The charging shifts of the iron nanoparticles are strongly influenced by the surrounding solvent. Hence, acetone exhibits the largest shift, water the smallest, and methanol in between. Dynamical measurements performed by application of the voltage stress in the form of SQW pulses gives information about the time constants of the processes involved, which led us postulate that these charging properties we probe in these systems, stem mainly from ionic movement(s).