Scientific Publications 2009
2009. "N-Terminal Enrichment: Developing a Protocol to Detect Specific Proteolytic Fragments." Journal of Biomolecular Techniques:JBT 20(5):263-265. Abstract Proteolytic processing events are essential to physiological processes such as reproduction, development, and host responses, as well as regulating proteins in cancer; therefore, there is a significant need to develop robust approaches for characterizing such events. The current mass spectrometry (MS)-based proteomics techniques employs a “bottom-up” strategy, which does not allow for identification of different proteolytic proteins since the strategy measures all the small peptides from any given protein. The aim of this development is to enable the effective identification of specific proteolytic fragments. The protocol utilizes an acetylation reaction to block the N-termini of a protein, as well as any lysine residues. Following digestion, N-terminal peptides are enriched by removing peptides that contain free amines, using amine-reactive silica-bond succinic anhydride beads. The resulting enriched sample has one N-terminal peptide per protein, which reduces sample complexity and allows for increased analytical sensitivity compared to global proteomics.1 We initially compared the peptide identification and efficiency of blocking lysine using acetic anhydride (a 42 Da modification) or propionic anhydride (a 56 Da modification) in our protocol. Both chemical reactions resulted in comparable peptide identifications and *95 percent efficiency for blocking lysine residues. However, the use of propionic anhydride allowed us to distinguish in vivo acetylated peptides from chemically-tagged peptides.2 In an initial experiment using mouse plasma, we were able to identify *300 unique N-termini peptides, as well as many known cleavage sites. This protocol holds potential for uncovering new information related to proteolytic pathways, which will assist our understanding about cancer biology and efforts to identify potential biomarkers for various diseases.
2009. "Characterizing and controlling the inherent dynamics of cyclophilin-A." Protein Science 18(4):811-824. doi:10.1002/pro.89 Abstract With the recent advances in NMR relaxation techniques, protein motions on functionally important timescales can be studied at atomic resolution. Here, we have used NMR-based relaxation experiments at several temperatures and both 600 and 900 MHz to characterize the inherent dynamics of the enzyme cyclophilin-A (CypA). We have discovered multiple chemical exchange processes within the enzyme that form a ‘‘dynamic continuum’’ that spans 20–30 A ˚ comprising active site residues and residues proximal to the active site. By combining mutagenesis with these NMR relaxation techniques, a simple method of counting the dynamically sampled conformations has been developed. Surprisingly, a combination of point mutations has allowed for the specific regulation of many of the exchange processes that occur within CypA, suggesting that the dynamics of an enzyme may be engineered.
2009. "Solution characterization of the extracellular region of CD147 and its interaction with its enzyme ligand cyclophilin-A." Journal of Molecular Biology 391(3):518-535. doi:10.1016/j.jmb.2009.05.080 Abstract The CD147 receptor plays an integral role in numerous diseases by stimulating the expression of several protein families and serving as the receptor for extracellular cyclophilins, however, neither CD147 nor its interactions with its cyclophilin ligands have been well characterized in solution. CD147 is a unique protein in that it can function both at the cell membrane and after being released from cells where it continues to retain activity. Thus, the CD147 receptor functions through at least two mechanisms that include both cyclophilin-independent and cyclophilin-dependent modes of action. In regard to CD147 cyclophilin-independent activity, CD147 homophilic interactions are thought to underlie its activity. In regard to CD147 cyclophilin-dependent activity, cyclophilin/CD147 interactions may represent a novel means of signaling since cyclophilins are also peptidyl-prolyl isomerases.
2009. "Density Functional Studies on the Complexation and Spectroscopy of Uranyl Ligated with Acetonitrile and Acetone Derivatives." Journal of Physical Chemistry A 113(45):12525-12531. Abstract The coordination of nitrile (acetonitrile, propionitrile, and benzonitrile) and carbonyl (formaldehyde, ethanal, and acetone) ligands to the uranyl dication (UO22+) has been examined using density functional theory (DFT) utilizing relativistic effective core potentials (RECPs). Complexes containing up to six ligands have been modeled for all ligands except formaldehyde, for which no minimum could be found. A comparison of relative binding energies indicates that five coordinate complexes are predominant while a six coordinate complex involving propionitrile ligands might be possible. Additionally, the relative binding energy and the weakening of the uranyl bond is related to the size of the ligand and, in general, nitriles bind more strongly to uranyl than carbonyls.
2009. "Application of SALSSA Framework to the Validation of Smoothed Particle Hydrodynamics Simulations of Low Reynolds Number Flows." Journal of Physics: Conference Series 180(1):Article No. 012065. doi:10.1088/1742-6596/180/1/012065 Abstract The Support Architecture for Large-Scale Subsurface Analysis (SALSSA) provides an extensible framework, sophisticated graphical user interface (GUI), and underlying data management system that simplifies the process of running subsurface models, tracking provenance information, and analyzing the model results. The SALSSA software framework is currently being applied to validating the Smoothed Particle Hydrodynamics (SPH) model. SPH is a three-dimensional model of flow and transport in porous media at the pore scale. Fluid flow in porous media at velocities common in natural porous media occur at low Reynolds numbers and therefore it is important to verify that the SPH model is producing accurate flow solutions in this regime. Validating SPH requires performing a series of simulations and comparing these simulation flow solutions to analytical results or numerical results using other methods. This validation study is being facilitated by the SALLSA framework, which provides capabilities to setup, execute, analyze, and administer these SPH simulations.
2009. "Rapid and Sustained Nuclear-Cytoplasmic ERK Oscillations Induced by Epidermal Growth Factor." Molecular Systems Biology 5:Article Number: 332. doi:10.1038/msb.2009.90 Abstract Mathematical modeling has predicted that ERK activity should oscillate in response to cell stimulation, but this has never been observed. To explore this inconsistency, we expressed an ERK1-GFP fusion protein in mammary epithelial cells. Following EGF stimulation, we observed rapid and continuous ERK oscillations between the nucleus and cytoplasm with a periodicity of approximately 15 minutes. These oscillations were remarkably persistent (>45 cycles), displayed an asymmetric waveform, and were highly dependent on cell density, essentially disappearing at confluency. We conclude that the ERK pathway is an intrinsic oscillator. Although the functional implications of the observed oscillations are uncertain, this property can be used to continuously monitor ERK activity in single cells.
2009. "The Corrosion of PEM Fuel Cell Catalyst Supports and Its Implications for Developing Durable Catalysts." Electrochimica Acta 54:3109-3114. Abstract Studying the corrosion behavior of catalyst support materials is of great significance for understanding the degradation of PEM fuel cell performance and developing durable catalysts. The oxidation of Vulcan carbon black (the most widely-used catalyst support for PEM fuel cells) was investigated using various electrochemical stressing methods (fixed-potential holding vs. potential step cycling), among which the potential step cycling was considered to mimic more closely the real drive cycle operation of vehicle PEM fuel cells. The oxidation of carbon was accelerated under potential step conditions as compared with the fixed-potential holding condition. Increasing potential step frequency or decreasing the lower potential limit in the potential step can further accelerate the corrosion of carbon. The accelerated corrosion of carbon black was attributed to the cycle of consumption/regeneration of some easily oxidized species. These findings are being employed to develop a test protocol for fast screening durable catalyst support.
2009. "The durability dependence of Pt/CNT electrocatalysts on the nanostructures of carbon nanotubes: hollow- and bamboo-CNTs." Journal of Nanoscience and Nanotechnology 9(10):5811-5815. Abstract The electrochemical durability of Pt/CNT with hollow- and bamboo-structured carbon nanotubes as the support for PEM fuel cells was investigated using cyclic voltammetry (CV, 0.6-1.1V) accelerated degradation test method. Pt/CNT catalysts were characterized with cyclic voltammograms, rotating disk electrodes, and TEM images. The changes in the electrochemical surface area of Pt and the activity toward oxygen reduction reaction (ORR) before and after the degradation indicate that bamboo-structured carbon nanotubes supported Pt (Pt/B-CNT) catalyst exhibited much higher durability. TEM images indicate that the sintering of Pt nanoparticles was much less for Pt/B-CNT. These are attributed to the specific bamboo-like nanostructures which provide more “bamboo-knot” defects and edge plane-like defects. Pt-support interaction was therefore enhanced and the durability was improved.
2009. "SO2-induced stability of Ag-alumina catalysts in the SCR of NO with methane." Applied Catalysis. B, Environmental 88(1-2):98-105. Abstract We report on a stabilization effect on the structure and activity of Ag/Al2O3 for the selective catalytic reduction (SCR) of NOx with CH4 imparted by the presence of SO2 in the exhaust gasmixture. The reaction is carried out at temperature above 600 8C to keep the surface partially free of sulfates. In SO2-free gases, catalyst deactivation is fast and measurable at these temperatures. Time-resolved TEM analyses of used samples have determined that deactivation is due to sintering of silver from well-dispersed clusters to nanoparticles to micrometer-size particles with time-on-stream at 625 8C. However, sintering of silver was dramatically suppressed by the presence of SO2 in the reaction gas mixture. The structural stabilization by SO2 was accompanied by stable catalyst activity for the NO reduction to N2. The direct oxidation of methane was suppressed, thus the methane selectivity was improved in SO2-laden gas mixtures. In tests with high-content silver alumina with some of the silver present in metallic form, an increase in the SCR activity was found in SO2-containing gas mixtures. This is attributed to redispersion of the silver particles by SO2, an unexpected finding. The catalyst performance was reversible over many cycles of operation at 625 8C with the SO2 switched on and off in the gas mixture.
2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233. doi:10.1128/IAI.00063-09 Abstract Macrophages plan important roles in controlling Salmonella-mediated systemic infection. To investigate the responses of macrophages to Salmonella infection, we infected RAW 264.7 macrophages with Salmonella enterica serovar Typhimurium (STM) and then performed a comparative liquid chromatography-tandem mass spectrometry [LC-MS(/MS)]-based proteomics analysis of the infected macrophages. A total of 1006 macrophage and 115 STM proteins were indentified from this study. Most of STM proteins were found at late stage of the time course of infection, consistent with the fact that STM proliferates inside RAW 264.7 macrophages. Majority of the identified macrophage proteins were house keeping-related, including cytoplasmic superoxide dismutase 1 (SOD1), whose peptide abundances were relatively constant during the time course of infection. Compared to those in no infection control, the peptide abundances of 244 macrophage proteins (or 24% of total indentified macrophage proteins) changed considerably after STM infection. The functions of these STM infection-affected macrophage proteins were diverse and ranged from production of antibacterial nitric oxide (i.e., inducible nitric oxide synthase or iNOS) or production of prostaglandin H2 (i.e., prostaglandin-endoperoxide synthase 2, also know as cyclooxygenase-2 or COX-2) to regulation of intracellular traffic (e.g., sorting nexin or SNX 5, 6 and 9), demonstrating a global impact of STM infection on macrophage proteome. Western-blot analysis not only confirmed the LC-MS(/MS) results of SOD1, COX-2 and iNOS, but also revealed that the protein abundances of mitochondrial SOD2 increased after STM infection, indicating an infection-induced oxidative stress in mitochondria.
2009. "Inhibition Effect of Secondary Phosphate Mineral Precipitation on Uranium Release from Contaminated Sediments." Environmental Science & Technology 43(21):8344-8349. doi:10.1021/es9021359 Abstract The inhibitory effect of phosphate mineral precipitation on uranium release was evaluated using a U(VI)-contaminated sediment collected from the US Department of Energy (DOE) Hanford site. The sediment contained U(VI) that was associated with diffusion-limited intragrain regions within its mm-size granitic lithic fragments. The sediment was first treated to promote phosphate mineral precipitation in batch suspensions spiked with 1 and 50 mM aqueous phosphate, and calcium in a stoichiometric ratio of mineral hydroxyapatite. The phosphate-treated sediment was then leached to solubilize contaminant U(VI) in a column system using a synthetic groundwater that contained chemical components representative of Hanford groundwater. Phosphate treatment significantly decreased the extent of U(VI) release from the sediment. Within the experimental duration of about 200 pore volumes, the effluent U(VI) concentrations were consistently lower by over one and two orders of magnitude after the sediment was treated with 1 and 50 mM of phosphate, respectively. Measurements of solid phase U(VI) using various spectroscopes and chemical extraction of the sediment collectively indicated that the inhibition of U(VI) release from the sediment was caused by: 1) U(VI) adsorption to the secondary phosphate precipitates and 2) the transformation of initially present U(VI) mineral phases to less soluble forms.
2009. "“Green" approach for self-assembly of platinum nanoparticles into nanowires in aqueous glucose solutions." Colloids and Surfaces. A, Physicochemical and Engineering Aspects 348(1-3):191-195 . Abstract A completely "green" synthetic approach has been developed for the reduction and stabilization of Pt nanoparticles followed by self-assembly into nanowires in an aqueous alpha-D-glucose solution. Hydrothermal treatment initiated the reduction of Pt(IV) ions dispersed in a pH 8.0 alpha-D-glucose solution in. Reduced Pt nanoparticles were stabilized with oxidized glucose molecules. The Pt nanoparticles continued growing into nanowires followed by transformation into cubic nanocrystals with a rough needle surface. Evidence from TEM and FT-IR spectra reveal that carboxylate groups, which are generated by the oxidation of alpha-D-glucose, strongly interact with and stabilize the surface of these Pt nanostructures.
2009. "A novel low-temperature dendritic cyclotrimerization of 2,6-diacetyl pyridine leading to mesoporous carbon containing pyridine rings." Microporous and Mesoporous Materials 123(1-3):345-348. doi:10.1016/j.micromeso.2009.03.033 Abstract A simple, direct synthesis of a mesoporous carbon containing pyridine rings is described. This synthesis utilizes the SiCl4 induced cyclotrimerization of 2,6-diacetylpyridine to make a dendritic polymer, built of alternating benzene and pyridine rings. The cyclotrimerization allows for a high degree of crosslinking to take place at low temperatures stabilizing the mesostructure and allowing the carbonization to be carried out at only 600°C, the lowest temperature reported to date for an N-doped mesoporous carbon. The functional mesoporous carbon so formed was found to have a surface area of 1275 m2/g, 35Å pores, and contain 6.8% N.
2009. "Controlled deposition of covalently bonded tantalum oxide on carbon supports by solvent evaporation sol-gel process." Surface Science 603(15):2290-2293. doi:10.1016/j.susc.2009.05.006 Abstract A simple strategy for covalently attaching Ta2O5 particles onto functionalized graphitic carbon supports has been developed to fabricate hybrid nanocomposites. In this process, tantalum ethoxide was directly reacted with functional groups on the carbon surface to form covalent bonding, which caused the carbonyl stretches of the carbon supports to be blue-shifted to 50-70 cm-1 after Ta2O5 particle deposition. Homogeneously distributed Ta2O5 particles with smaller than 100 nm have been homogeneously deposited on the carbon supports. X-ray diffraction (XRD), FT-IR spectroscopy, and scanning electron microscopy (SEM) have been used to study the formation of Ta2O5/C hybrid structure.
2009. "Ultrafast Differential Ion Mobility Spectrometry at Extreme Electric Fields Coupled to Mass Spectrometry." Analytical Chemistry 81(19):8048-8053. doi:10.1021/ac901479e Abstract Microchip-based field asymmetric waveform ion mobility spectrometry (FAIMS) analyzers featuring a grid of 35 μm - wide channels have allowed electric field intensity (E) over 60 kV/cm, or about twice that in previous devices with >0.5 mm gaps. Since separation speed scales as E4 to E6, these chips filter ions in just ~20 μs (or ~100 - 10,000 times faster than “macroscopic” designs), although with reduced resolution. Here we report integration of these chips into electrospray ionization (ESI) mass spectrometry, with ESI coupled to FAIMS via a curtain plate/orifice interface with edgewise ion injection into the gap. Adjusting gas flows in the system permits control of ion residence time in FAIMS that affects resolving power independently of ion desolvation after the ESI source, and the results agree with a priori simulations and scaling rules. Exemplary applications include analyses of amino acids, peptides, and whole proteins. Because of limited resolving power, present FAIMS is mostly useful for distinguishing compound classes rather than species within them. In particular, peptides separate from other ions, and large proteins fully separate from smaller proteins and peptides (likely because the field in FAIMS reversibly aligns the macroions with sufficiently strong electric dipoles).
2009. "The [(AI2O3)2]- Anion Cluster: Electron Localization-Delocalization Isomerism." Chemphyschem 10(14):2410-2413. Abstract Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling.[1,2] Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters.[3,4] Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts.[5-8] In particular, the [(Al2O3)3-5]+ clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH4. Over the past decades gas phase aluminum oxide clusters have been extensively studied both experimentally[3,4,7-10] and computationally,[3,4,7,11-14] but definitive structural assignments were made for only a handful of them: the planar [Al3O3]− and [Al5O4]− cluster anions, [9c,13f] and the [(Al2O3)1-4(AlO)]+ cluster cations. For stoichiometric clusters only the atomic structures of [(Al2O3)4]+/0 have been nambiguously resolved. Here we report on the structures of the [(Al2O3)2]−/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al2O3)2]− cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.
2009. "Surface energies, work functions, and surface relaxations of low index metallic surfaces from first principles." Physical Review. B, Condensed Matter and Materials Physics 80(23):Article No. 235407. doi:10.1103/PhysRevB.80.235407 Abstract We study the relaxations, surface energies, and work functions of low-index metallic surfaces using pseudopotential plane-wave density-functional calculations within the generalized gradient approximation. We study here the (100), (110), and (111) surfaces of Al, Pd, Pt, and Au and the (0001) surface of Ti, chosen for their use as contact or lead materials in nanoscale devices. We consider clean, mostly nonreconstructed surfaces in the slab-supercell approximation. Particular attention is paid to the convergence of these quantities with respect to slab thickness; furthermore, different methodologies for the calculation of work functions and surfaces energies are compared. We find that the use of bulk references for calculations of surface energies and work functions can be detrimental to convergence unless numerical grids are closely matched, especially when surface relaxations are being considered. Our results and comparison show that calculated values often do not quantitatively match experimental values. This may be understandable for the surface relaxations and surface energies, where experimental values can have large error but even for the work functions, neither local nor semilocal functionals emerge as an accurate choice for every case.
2009. "Kinetics for Tautomerizations and Dissociations of Triglycine Radical Cations." Journal of the American Society for Mass Spectrometry 20(6):996-1005. Abstract Fragmentations of tautomers of the α-centered radical triglycine radical cation, [GGG*]+, [GG*G]+, and [G*GG]+, are charge-driven, giving b-type ions; these are processes that are facilitated by a mobile proton, as in the fragmentation of protonated triglycine (Rodriquez, C.F. et al. J. Am. Chem. Soc. 2001, 123, 3006 - 3012). By contrast, radical centers are less mobile. Two mechanisms have been examined theoretically utilizing density functional theory and Rice-Ramsperger-Kassel-Marcus modeling: (1) a direct hydrogen-atom migration between two α-carbons, and (2) a two-step proton migration involving a canonical [GGG]*+ as an intermediate. Predictions employing the latter mechanism are in good agreement with results of recent CID experiments (Chu, I.K. et al. J. Am. Chem. Soc. 2008, 130, 7862 - 7872).
2009. "Molecular Characterization of Biomass Burning Aerosols Using High Resolution Mass Spectrometry." Analytical Chemistry 81(4):1512-1521. doi:10.1021/ac8020664 Abstract Chemical characterizations of atmospheric aerosols is a serious analytical challenge because of the complexity of particulate matter analyte composed of a large number of compounds with a wide range of molecular structures, physico-chemical properties, and reactivity. In this study chemical composition of biomass burning organic aerosol (BBOA) samples is characterized by high resolution electrospray ionization mass spectrometry (ESI/MS). Accurate mass measurement combined with Kendrick analysis allowed us to assign elemental composition for hundreds of compounds in the range of m/z values of 50-1000. ESI/MS spectra of different BBOA samples contain a variety of distinct, sample specific, characteristic peaks that can be used as unique markers for different types of biofuels. Our results indicate that a significant number of high-MW organic compounds in BBOA samples are highly oxidized polar species that can be efficiently detected using ESI/MS but are difficult to observe using the conventional GCMS analysis of aerosol samples. The average O:C ratios obtained for each of the BBOA samples studied in this work are in a strikingly good agreement with the previously reported values obtained using STXM/NEXAFS. The degree of unsaturation of detected organic compounds shows a clear decrease with increase in the molecular weight of the anyalyte molecules. The decrease is particularly pronounced for the samples containing a large number of CH2-based homologous series.
2009. "The Effect of the Incident Collision Energy on the Porosity of Vapor Deposited Amorphous Solid Water Films." Journal of Physical Chemistry B 113(13):4000-4007. Abstract Molecular beam techniques are used to grow water films on Pt(111) with various incident angles and collision energies from 5 to 205 kJ/mole. The effect of the incident angle and collision energy on the porosity and surface area of the vapor deposited water films was studied using nitrogen physisorption and infrared spectroscopy. At low incident energy (5 kJ/mole), the infrared spectra, which provide a direct measure of the surface area, show that the surface area increases with incident angle and levels-off at angles > 65°. This is in contrast to the nitrogen uptake data which display a maximum near 70° due to the decrease in nitrogen condensation in the larger pores that develop at high incident angles. Both techniques show that the morphology of vapor deposited water films depends strongly on the incident kinetic energy. These observations are consistent with a ballistic deposition-shadowing model used to describe the growth of highly porous materials at glancing angle. The dependence of film morphology on incident energy may have important implications for the growth of porous materials via glancing angle deposition and for the structure of interstellar ices.
2009. "Uranium Extraction From Laboratory Synthesized, Uranium-Doped Hydrous Ferric Oxides ." Environmental Science & Technology 43:2341-2347. Abstract The extractability of uranium (U) from synthetic hydrous ferric oxides has been shown to decrease as a function of mineral ripening, consistent with the hypothesis that the ripening process decrease contaminant lability. To evaluate this process, three hydrous ferric oxide (HFO) suspensions were co-precipitated with uranyl (UO22+) and maintained at pH 7.0 ± 0.1. Uranyl was added to the HFO post-precipitation in a fourth suspension. Two suspensions also contained either co-precipitated silicate (Si-U-HFO) or phosphate (P-U-HFO). After precipitation of the HFOs, at time intervals of one week, one month, six months, one year, and 2 years, aliquots of the suspensions were contacted with five solutions for a range of time. The extracts were analyzed for U and iron (Fe). The results are consistent with the hypothesis that U and Fe extractability will decrease as the mineral phase ripens. All extracting solutions exhibited some degree of selectivity for U, as the proportional extraction of U exceeded that for congruent dissolution. Micro X-ray diffraction analysis indicates the transformation from an amorphous phase to a material containing substantial proportions of crystalline goethite and hematite, except the P-U-HFO which remained primarily amorphous. Further analysis of the co-precipitates by the Mössbauer technique and scanning electron microscopy (SEM) provides further evidence of mineralogic ripening
2009. "Experimental and Computational Studies of the Macrocyclic Effect of an Auxiliary Ligand on Electron and Proton Transfers Within Ternary Copper(II)–Histidine Complexes ." Journal of the American Society for Mass Spectrometry 20(6):972-984. Abstract The dissociation of [CuII(L)His]•2+ complexes [L = diethylenetriamine (dien) or 1,4,7-triazacyclononane (9-aneN3)] bears a strong resemblance to the previously reported behavior of [CuII(L)GGH]•2+ complexes. We have used low energy collision-induced dissociation experiments and density functional theory (DFT) calculations at the B3LYP/6-31+G(d) level to study the macrocyclic effect of the auxiliary ligands on the formation of His•+ from prototypical [CuII(L)His]•2+ systems. DFT revealed that the relative energy barriers of the same electron transfer (ET) dissociation pathways of [CuII(9-aneN3)His]•2+ and [CuII(dien)His]•2+ are very similar, with the ET reactions of [CuII(9-aneN3)His]•2+ leading to the generation of two distinct His•+ species; in contrast, the proton transfer (PT) dissociation pathways of [CuII(9-aneN3)His]•2+ and [CuII(dien)His]•2+ differ considerably. The PT reactions of [CuII(9-aneN3)His]•2+ are associated with substantially higher barriers (>13 kcal/mol) than those of [CuII(dien)His]•2+. Thus, the sterically encumbered auxiliary 9-aneN3 ligand facilitates ET reactions while moderating PT reactions, allowing the formation of hitherto non-observable histidine radical cations.
2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105. Abstract The northwestern Sargasso Sea is part of the North Atlantic subtropical oceanic gyre that is characterized as seasonally oligotrophic with pronounced stratification in the summer and autumn. Essentially a marine desert, the biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorous and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary LC-tandem mass spectrometry to study the composition of microbial proteomes in surface samples collected in September 2005. A total of 2279 peptides that mapped to 236 SAR11 proteins, and 3208 peptides that mapped to 404 Synechococcus proteins, were detected. Mass spectra from SAR11 periplasmic binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars, and spermidine. Although the data showed that a large fraction of microbial protein synthesis in the Sargasso Sea is devoted to inorganic and organic nutrient acquisition, the proteomes of both SAR11 and Synechococcus also indicated that these populations were actively growing. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme but sufficient to sustain microbial community activity.
2009. "Rapid Measurement of Emissions from Military Aircraft Turbine Engines by Downstream Extractive Sampling of Aircraft on the Ground: Results for C-130 and F-15 Aircraft." Atmospheric Environment 43(16):2612-2622. doi:10.1016/j.atmosenv.2009.02.012 Abstract Aircraft emissions affect air quality on scales from local to global. About 10% of the aviation fuel used in the U.S. is consumed by military aircraft, and emissions from this source are facing increasingly stringent environmental regulations, so improved methods for quickly and accurately determining emissions from existing and new engines are needed. This paper reports results of a study to advance the methods used for detailed characterization of military aircraft emissions, and provides emission factors for two aircraft; the F-15 fighter and the C-130 cargo plane. The new approach employs a strategy of outdoor ground-level sampling downstream behind operational military aircraft. This permits rapid change-out of the aircraft so that engines can be tested quickly on operational aircraft Measurements were made at throttle settings from idle to afterburner using a simple extractive probe in the dilute exhaust. Emission factors determined using this approach agree very well with those from the traditional method of extractive sampling at the exhaust exit. Emission factors are reported for CO2, CO, NO, NOx, and more than 60 hazardous and/or reactive organic gases. Intra-engine and engine to engine variability were assessed. For both engines, the effect of engine power on emissions was as expected, with higher power leading to reduced emission factors for CO and organic gases and higher emission factors for nitrogen oxides. At afterburner power, the F-15 engine yielded higher emission factors for CO and many organics and lower NOx emission factors compared with the military power throttle setting. The C-130 turboprop engine generally produced higher CO andorganic emissions and lower NOx emissions per unit of fuel consumed than the F-15 engines. Comparison of the emissions of nine hazardous air pollutants from these two engines with emissions from nine other aircraft engines also is discussed.
2009. "Fragmentation Mechanisms of Oxidized Peptides Elucidated by SID, RRKM Modeling and Molecular Dynamics." Journal of the American Society for Mass Spectrometry 20(9):1579-1592. doi:10.1016/j.jasms.2009.04.012 Abstract The gas phase fragmentation reactions of singly charged angiotensin II (AngII, DRVYIHPF) and the ozonolysis products AngII+O (DRVY*IHPF), AngII+3O (DRVYIH*PF), and AngII+4O (DRVY*IH*PF) were studied using SID FT-ICR mass spectrometry and molecular dynamics. Oxidation of Tyr (AngII+O) leads to an additional low-energy charge-remote selective fragmentation channel resulting in the b4 fragment ion. Modification of His leads to a series of new selective dissociation channels. For AngII+3O and AngII+4O, the formation of [MH+3O]+-45 and [MH+3O]+-71 are driven by charge-remote processes while it is suggested that the b5 and [MH+3O]+-88 fragments are a result of charge-directed reactions. Energy-resolved SID experiments and RRKM modeling were able to provide insight into the energetics of the lowest energy fragmentation channel for each of the parent ions. Destabilization of the ozonolysis products was found to be strictly due to entropic effects. Mechanistic details for each of the new dissociation pathways were determined by relating the SID FT-ICR MS results to parent ion conformations samples using molecular dynamics.
2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8(5):2261-2272. Abstract Human platelets play a key role in homeostasis and thrombosis and have recently emerged as key regulators of inflammation. Platelets stored for transfusion produce pro-thrombotic and pro-inflammatory mediators implicated in adverse transfusion reactions. Correspondingly, these mediators are central players in pathological conditions including cardiovascular disease, the major cause of death in diabetics. In view of this, a mass spectrometry based proteomics study was performed on platelets collected from healthy and type-2 diabetics stored for transfusion. Strikingly, our innovative and sensitive proteomic approach identified 146 proteins that were either up- or down-regulated in type-2 diabetics relative to non-diabetic controls, 151 proteins whose abundances changed during a 5-day storage period and 22 proteins whose abundance changed after 5-days of storage were only observed in samples from diabetics. Notably our studies are the first to characterize the proteome of platelets from diabetics before and after storage for transfusion. These identified differences allow us to formulate new hypotheses and experimentation to improve clinical outcomes by targeting "high risk platelets" that render platelet transfusion less effective or even unsafe.
2009. "The Use of Auger Spectroscopy for the in situ Elemental Characterization of Sub-micrometer Presolar Grains." Meteoritics and Planetary Science 44(7):1033-1049. Abstract Presolar grains are small samples of stardust which can be found at low abundances in some of the most unaltered types of extraterrestrial materials. These grains condensed in the environments of massive stars before the formation of the solar system and survived incorporation into solar system materials without completely losing their isotopic, elemental and mineralogical makeup. Laboratory analyses of these presolar grains give insights into stellar nucleosynthesis and provide clues about the physical and chemical conditions during their formation as well as about interstellar exposure history and parent body processes. Since most presolar grains are less than 1 micrometer in diameter and represent only a few ppm of their host materials (e.g., meteorites or interplanetary dust particles), locating and studying these particles can be analytically challenging. Recently, we began using scanning Auger spectroscopy for the in situ elemental characterization of presolar grains and found that this technique, especially when paired with spatially matched NanoSIMS isotopic studies, can provide important insights that would be difficult to obtain with other analytical approaches. Here we discuss details of applying Auger spectroscopy to sub-micrometer sized geological samples and address practical issues such as sample preparation, measurement settings, data processing, and elemental quantification.
2009. "Single-step conversion of cellulose to 5-hydroxymethylfurfural (HMF), a versatileplatform chemical." Applied Catalysis. A, General 361(1-2):117-122. doi:10.1016/j.apcata.2009.04.002 Abstract The ability to use cellulosic biomass as feedstock for the production of fuels and chemicals currently derived from petroleum depends critically on the development of effective low-temperature processes. While HMF, as a versatile platform chemical suitable for use in polymer synthesis or production of liquid biofuels, can currently be made from fructose and glucose, synthesis of HMF directly from raw natural cellulose represents the last major barrier toward the development of a sustainable HMF platform. Here we report an unprecedented single-step pathway that depolymerizes cellulose rapidly under mild conditions and converts the resulting glucose to hydroxymethylfurfural (HMF). A pair of metal chlorides (CuCl2 and CrCl2) dissolved in 1-ethyl-3-methylimidazolium chloride at temperatures of 80-120°C catalyzes cellulose depolymerization and the subsequent glucose conversion to HMF with 95% selectivity among recoverable products (at 56% HMF yield). Cellulose depolymerization, which can also be catalyzed by other metalchloride pairs such as CuCl2 paired with PdCl2, CrCl3, or FeCl3, occurs at a rate that is more than one order of magnitude faster than conventional acid-catalyzed hydrolysis. In contrast, single-metal chlorides at the same total loading showed low activity under similar conditions. Mechanistic studies suggest that the C2 hydrogen of the imidazolium ring is activated by the paired metal-chloride catalysts.
2009. "Semiexperimental Equilibrium Structure for the C₆ Backbone of cis-1,3,5-Hexatriene;Structural Evidence for Greater π-Electron Delocalization with Increasing Chain Length in Polyenes." Journal of Physical Chemistry A 113(9):1864-1868. doi:10.1021/jp8106777 Abstract Twenty-five microwave lines were observed for cis-1,3,5-hexatriene (0.05 D dipole moment) and a smaller number for its three 13C isotopomers in natural abundance. Ground-state rotational constants were fitted for all four species to a Watson-type rotational Hamiltonian for an asymmetric top (κ ) -0.9768). Vibration-rotation (alpha) constants were predicted with a B3LYP/cc-pVTZ model and used to adjust the ground-state rotational constants to equilibrium rotational constants. The small inertial defect for cis-hexatriene shows that the molecule is planar, despite significant H-H repulsion. The substitution method was applied to the equilibrium rotational constants to give a semiexperimental equilibrium structure for the C6 backbone. This structure and one predicted with the B3LYP/cc-pVTZ model show structural evidence for increased π-electron delocalization in comparison with butadiene, the first member of the polyene series.
2009. "A High Yield Synthesis of Chalcopyrite CuInS2 Nanoparticles with Exceptional Size Control." Journal of Nanomaterials 2009:Article No. 748567. doi:10.1155/2009/748567 Abstract Various I-III-VI2 semiconductor materials have been identified as promising photovoltaic materials [1, 2]. Recently, quantum dot (QD) based solar cells have attracted much attention due to their potential to replace thin film devices [3-5]. One of the major advantages of employing QDs is by simply changing the particle size they can be tuned to absorb specific wavelengths ranging from visible to infrared wavelengths . Furthermore, with careful design of photovoltaic (PV) devices incorporating various sizes of nanoparticles in multiple layers, one may achieve increased solar energy absorption in one device [7, 8]. In order to facilitate QD based multilayer devices, synthetic strategies that can deliver QDs in high yields with precise size control are essential. One of the strategies to prepare QDs is to prepare nanoparticles from molecular single source precursors (SSPs), which contain all necessary elements in a single molecule. In recent years, there have been several reports on the formation of CuInS2 nanoparticles through the decomposition of SSPs using thermolysis [9-14], photolysis , and microwave irradiation . However, many of these procedures require a combination of long reaction times (10 to 24 hours) and high reaction temperatures (often exceeding 200 °C) with very little information regarding overall yields. Microwave-assisted growth of nanoparticles is generally favorable over traditional thermolysis as microwave irradiation overcomes local intermediaries and increases the microscopic temperature of the reaction  thus exhibiting greater homogeneity in the overall reaction temperature. This allows for nanoparticles with diameters of a few nanometers can be prepared , dramatic decreases in reaction times, improved product purities, all forms of precursors can be used, and reactions exhibit high reproducibility and yields . For CuInS2 QDs, the Wannier-Mott bulk exciton radius is approximately 8 nm with a bandgap of 1.45 eV and QDs with radii smaller than 8 nm exhibit bandgaps greater than 1.45 eV . Our group has recently reported the synthesis of CuInS2 nanoparticles using SSPs via microwave irradiation with 1-hexanethiol as a surface pacifying ligand to afford nanoparticle sizes ranging from 3 to 5 nm . Herein, we report efficient size controlled syntheses of Chalcopyrite CuInS2 nanoparticles by decomposition of SSPs in the presence of 1,2-ethanedithiol with extraordinarily high yields. The titration studies by 1H NMR using SSP 1 with 1,2-ethanedithiol and benzyl mercaptan are conducted to elucidate the formation of Chalcopyrite CuInS2 nanoparticles.
2009. "Solid-State and Solution NMR Studies of the CAP-Gly Domain of Mammalian Dynactin and Its Interaction with Microtubules." Journal of the American Chemical Society 131(29):10113-10126. doi:10.1021/ja902003u Abstract Microtubules (MTs) and microtubule binding proteins (MTBPs) play fundamental physiological roles including vesicle and organelle transport, cell motility, and cell division. Despite the importance of the MT/MTBP assemblies, there remains virtually no structural or dynamic information about their interaction at the atomic level due to the inherent insolubility and lack of long-range order of MTs. In this study, we present a combined magic angle spinning solid-state and solution NMR study of the MTBP CAP-Gly domain of mammalian dynactin and its interaction with paclitaxel-stabilized microtubules. We report resonance assignments and secondary structure analysis of the free CAP-Gly in solution and in the solid state by a combination of two- and three-dimensional homo- and heteronuclear correlation spectra. In solution, binding of CAP-Gly to microtubules is accompanied by the broadening of the majority of the peaks in HSQC spectra except for the residues at the termini, precluding further structural analysis of the CAP-Gly/microtubule complexes. In the solid state, DARR spectra of free CAP-Gly and its complex with microtubules display well-resolved lines, permitting residue-specific resonance assignments. Interestingly, a number of chemical shifts in the solid-state DARR spectra of the CAP-Gly/microtubule complex are perturbed compared to those of the free CAP-Gly, suggesting that conformational changes occur in the protein upon binding to the microtubules. These results indicate that CAP-Gly/microtubule assemblies are amenable to detailed structural characterization by magic angle spinning NMR spectroscopy and that solid-state NMR is a viable technique to study MT/protein interactions in general.
2009. "Diversity of Functionalized Germanium Zintl Clusters: Syntheses and Theoretical Studies of [Ge9PdPPh3]3- and [Ni@(Ge9PdPPh3)]2-." Journal of Cluster Science 20(3):601-609. doi:10.1007/s10876-009-0266-1 Abstract A new Zintl cluster [Ge9PdPPh3]3- has been isolated as (2,2,2-crypt)K+ salt through the reaction of K4Ge9 and Pd[PPh3]4 in ethylenediamine solutions and characterized via single-crystal X-ray crystallography. The as-prepared bimetallic [Ge9PdPPh3]3- cluster could successfully trap a nickel atom to form a trimetallic cluster [Ni@(Ge9PdPPh3)]2-. The coordination of Ge94- by PdPPh3 induces a one-electron oxidation and encapsulation of the Ni atom into the Ge93- cage leads to a further one-electron oxidation and a geometry transformation from C4v (nido) to C3v (closo).