Scientific Publications 2010
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2010. "Effect of the Basic Residue on the Energetics, Dynamics and Mechanisms of Gas- Phase Fragmentation of Protonated Peptides." Journal of the American Chemical Society 132(45):16006-16016. doi:10.1021/ja104438z Abstract The effect of the basic residue on the energetics, dynamics and mechanisms of backbone fragmentation of protonated peptides was investigated. Time- and collision energy-resolved surface-induced dissociation (SID) of singly protonated peptides with the N-terminal arginine residue and their analogs, in which arginine is replaced with less basic lysine and histidine residues was examined using in a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). SID experiments demonstrated very different kinetics of formation of several primary product ions of peptides with and without arginine residue. The energetics and dynamics of these pathways were determined from the RRKM modeling of the experimental data. Comparison between the kinetics and energetics of fragmentation of arginine-containing peptides and the corresponding methyl ester derivatives provides important information on the effect of dissociation pathways involving salt bridge (SB) intermediates on the observed fragmentation behavior. It is found that because pathways involving SB intermediates are characterized by low threshold energies, they efficiently compete with classical oxazolone pathways of arginine-containing peptides on a long timescale of the FT-ICR instrument. In contrast, fragmentation of histidine- and lysine-containing peptides is largely determined by classical oxazolone pathways. Because SB pathways are characterized by negative activation entropies, fragmentation of arginine-containing peptides is kinetically hindered and observed at higher collision energies as compared to their lysine- and histidine-containing analogs.
2010. "Fragmentation of alpha-Radical Cations of Arginine-Containing Peptides." Journal of the American Society for Mass Spectrometry 21(4):511-521. doi:10.1016/j.jasms.2009.12.021 Abstract Fragmentation pathways of peptide radical cations, M+, with well-defined initial location of the radical site were explored using collision-induced dissociation (CID) experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes [salen = N,N´-ethylenebis (salicylideneaminato)]. Subsequent hydrogen abstraction from the -carbon of the side chain followed by Ca-C bond cleavage results in the loss of a neutral side chain and formation of an a-radical cation with the radical site localized on the a-carbon of the backbone. Similar CID spectra dominated by radical-driven dissociation products were obtained for a number of a-radicals when the basic arginine side chain was present in the sequence. In contrast, proton-driven fragmentation dominates CID spectra of a-radicals produced via the loss of the arginine side chain. Our results suggest that in most cases radical migration precedes fragmentation of large peptide radical cations.
2010. "High-Resolution Desorption Electrospray Ionization Mass Spectrometry for Chemical Characterization of Organic Aerosols." Analytical Chemistry 82(5):2048-2058. doi:10.1021/ac902801f Abstract Characterization of the chemical composition and chemical transformations of secondary organic aerosol (SOA) is both a major challenge and the area of greatest uncertainty in current aerosol research. This study presents the first application of desorption electrospray ionization combined with high-resolution mass spectrometry (DESI-MS) for detailed chemical characterization and studies of chemical aging of OA collected on Teflon substrates. DESI-MS offers unique advantages both for detailed characterization of chemically labile components in OA that cannot be detected using more traditional electrospray ionization mass spectrometry (ESI-MS) and for studying chemical aging of OA. DESI-MS enables rapid characterization of OA samples collected on substrates by eliminating the sample preparation stage. In addition, it enables detection and structural characterization of chemically labile molecules in OA samples by minimizing the residence time of analyte in the solvent. SOA produced by the ozonolysis of limonene (LSOA) was allowed to react with gaseous ammonia. Chemical aging resulted in measurable changes in the optical properties of LSOA observed using UV- visible spectroscopy. DESI-MS combined with tandem mass spectrometry experiments (MS/MS) enabled identification of species in aged LSOA responsible for absorption of the visible light. Detailed analysis of the experimental data allowed us to identify chemical changes induced by reactions of LSOA constituents with ammonia and distinguish between different mechanisms of chemical aging.
2010. "Soft-Landing of CoIII(salen)+ and MnIII(salen)+ on Self-Assembled Monolayer Surfaces." Journal of Physical Chemistry C 114(12):5305-5311. doi:10.1021/jp904384q Abstract Soft-landing of mass-selected CoIII(salen)+ and MnIII(salen)+ complexes was performed using self-assembled monolayer surfaces of alkanethiol (HSAM) and fluorinated alkanethiol (FSAM) on gold as targets. Physical processes associated with ion deposition were studied using time-resolved in situ secondary ion mass spectrometry (SIMS) in a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). We demonstrate charge retention by a significant fraction of precursor ions on the FSAM and complete neutralization on the HSAM surface. Our results indicate efficient electron transfer from gold to the deposited species for the HSAM surface and inefficient, if any, electron transfer on the FSAM surface. Formation of abundant cluster ions observed in SIMS spectra is attributed to gas-phase reactions in the SIMS plume. Detailed analysis allowed us to extract the kinetics of both ionic and neutral complexes trapped on the FSAM surface. The results indicate that neutralization on this surface most likely takes place on the defect sites.
2010. "The effect of PdZn particle size on reverse-water-gas-shift reaction ." Applied Catalysis. A, General 379(1-2):3-6. Abstract The effect of PdZn particle size on the catalytic activity of Pd/ZnO catalysts for the reverse-water-gas-shift (RWGS) reaction was studied. The PdZn particle size was varied by adjusting Pd loading and reducing the catalysts at different temperatures. XRD and IR spectroscopy characterization confirmed the absence of metallic Pd on the catalyst surface. Consequently, the effect of PdZn alloy particle size on the RWGS reaction can be unambiguously studied without the complication of reactions catalyzed by metallic Pd. The results indicated that the turnover frequency increases as the PdZn crystallite size decreases. Interestingly, this structure relationship between PdZn particle size and RWGS activity is consistent with that previously observed for the steam reforming of methanol, i.e., higher CO selectivity on smaller PdZn particles. Thus, RWGS has been identified as a likely potential reaction pathway to undesired CO formation in methanol steam reforming on Pd/ZnO catalysts for hydrogen production.
2010. "Oxidative Decomposition of Methanol on Subnanometer Palladium Clusters: The Effect of Catalyst Size and Support Composition." Journal of Physical Chemistry C 114(23):10342-10348. doi:10.1021/jp912220w Abstract Size and support effects in the oxidative decomposition of methanol on amorphous alumina supported subnanometer palladium clusters were studied under realistic reaction conditions of pressure and temperature. The smaller Pd8-12 clusters were found to promote the decomposition channel to CO and hydrogen, however with mediocre activity due to poisoning. The larger Pd15-18 clusters preferentially produce dimethyl ether and formaldehyde, without signs of posioning. A thin titania overcoat applied on the Pd15-18 improves the sintering-resistance of the catalyst. Accompanying density functional calculations confirm the posioning of small Pd clusters by CO.
2010. "Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1." Journal of Molecular Biology 401(3):334-49. Abstract Precise 3′-end processing of mRNA is essential for correct gene expression, yet in yeast, 3′-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3′-processing and are recognized by the RNAbinding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein–protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3′-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.
2010. "Increased Silver Activity for Direct Propylene Epoxidation via Subnanometer Size Effects." Science 328(5975):224-228. doi:10.1126/science.1185200 Abstract Production of the industrial chemical propylene oxide is energy-intensive and environmentally unfriendly. Catalysts based on bulk silver surfaces with direct propylene epoxidation by molecular oxygen have not resolved these problems because of substantial formation of carbon dioxide. We found that unpromoted, size-selected Ag3 clusters and ~3.5-nanometer Ag nanoparticles on alumina supports can catalyze this reaction with only a negligible amount of carbon dioxide formation and with high activity at low temperatures. Density functional calculations show that, relative to extended silver surfaces, oxidized silver trimers are more active and selective for epoxidation because of the open-shell nature of their electronic structure. The results suggest that new architectures based on ultrasmall silver particles may provide highly efficient catalysts for propylene epoxidation.
2010. "Identification of an Unconventional E3 Binding Surface on the UbcH5 ∼ Ub Conjugate Recognized by a Pathogenic Bacterial E3 Ligaseby a pathogenic bacterial E3 ligase." Proceedings of the National Academy of Sciences of the United States of America 107(7):2848-2853. doi:10.1073/pnas.0914821107 Abstract Gram-negative bacteria deliver a cadre of virulence factors directly into the cytoplasm of eukaryotic host cells to promote pathogenesis and/or commensalism. Recently, families of virulence proteins have been recognized that function as E3 Ubiquitin-ligases. How these bacterial ligases integrate into the ubiquitin (Ub) signaling pathways of the host and how they differ functionally from endogenous eukaryotic E3s is not known. Here we show that the bacterial E3 SspH2 from S. typhimurium selectively binds the human UbcH5 ∼ Ub conjugate recognizing regions of both UbcH5 and Ub subunits. The surface of the E2 UbcH5 involved in this interaction differs substantially from that defined for other E2/E3 complexes involving eukaryotic E3-ligases. In vitro, SspH2 directs the synthesis of K48-linked poly-Ub chains, suggesting that cellular protein targets of SspH2-catalyzed Ub transfer are destined for proteasomal destruction. Unexpectedly, we found that intermediates in SspH2-directed reactions are activated poly-Ub chains directly tethered to the UbcH5 active site (UbcH5 ∼ Ubn). Rapid generation of UbcH5 ∼ Ubn may allow for bacterially directed modification of eukaryotic target proteins with a completed poly-Ub chain, efficiently tagging host targets for destruction.
2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390. doi:10.1038/msb.2010.47 Abstract After hundreds of generations of mid log phase growth, Escherichia coli acquires a higher growth rate as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). FBA solutions contain hundreds of variables that can be examined using omics methods. We report that 99% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the resulting evolved strains reinforce the optimal growth predictions. Specifically, through constraint-based analysis of the proteomic and transcriptomic data, we find: 1) selective pressure for the predicted optimal growth states and a minimization of network flux; 2) suppression of genes outside of the optimal growth solutions; and 3) a trend towards usage of more efficient metabolic pathways. For processes not in GEMs, we find 4) an increase in the transcription/translation machinery and stringent response suppression, and 5) that established regulons are significantly down-regulated. Thus, differential expression supports observed growth phenotype changes, and observed expression in evolved strains is consistent with GEM computed optimal growth states.
2010. "Catalyst Structure-Performance Relationship Identified by High-Throughput Operando Method: New Insight for Silica-Supported Vanadium Oxide for Methanol Oxidation." Topics in Catalysis 53(1-2):40-48. Abstract A prototype high throughput operando reactor, that integrates FT-IR imaging for rapid reaction product analysis and parallel Raman imaging for catalyst characterization, has been designed to accelerate catalyst discovery and, concurrently, fundamental research toward reliable correlations between catalyst active sites and catalyst performance for at-line real catalytic conditions. This reactor, consisting of six parallel reaction channels, is demonstrated for methanol oxidation using silica supported vanadium oxide catalysts at various reaction conditions. The results of semi-quantitative analysis of a large array of operando Raman scattering bands, specifically for C−H bonds in Si−OCH3 and V−OCH3 surface intermediates, obtained simultaneously on multiple catalyst surfaces with a time resolution of 60s for each set at different temperatures, reveal for the first time methanol activation at surface vanadium oxide cluster edge on silica support at lower reaction temperatures, <175°C. This activation phenomenon is not observed at a higher reaction temperature, 225°C.
2010. "Theoretical Investigations on the Formation and Dehydrogenation Reaction Pathways of H(NH2BH2)nH (n=1-4) Oligomers: Importance of Dihydrogen Interactions (DHI)." Inorganic Chemistry 49(17):7710-7720. Abstract The H(NH2BH2)nH oligomers are possible products from dehydrogenation of ammonia borane (NH3BH3) and ammonium borohydride (NH4BH4), which belong to a class of boron-nitrogen-hydrogen (BNHx) compounds that are promising materials for chemical hydrogen storage. Understanding the kinetics and reaction pathways of formation of these oligomers and their further dehydrogenation is essential for developing BNHx-based hydrogen storage materials. We have performed computational modeling using density functional theory (DFT), ab initio wavefunction theory, and Car-Parrinello molecular dynamics (CPMD) simulations on the energetics and formation pathways for the H(NH2BH2)nH (n=1-4) oligomers, polyaminoborane (PAB), from NH3BH3 monomers and the subsequent dehydrogenation steps to form polyiminoborane (PIB). Through transition state searches and evaluation of the intrinsic reaction coordinates, we have investigated the B-N bond cleavage, the reactions of NH3BH3 molecule with intermediates, dihydrogen release through intra- and intermolecular hydrogen transfer, dehydrocoupling/cyclization of the oligomers, and the dimerization of NH3BH3 molecules. We discovered the formation mechanism of H(NH2BH2)n+1H oligomers through reactions of the H(NH2BH2)nH oligomers first with BH3 followed by reactions with NH3 and the release of H2, where the BH3 and NH3 intermediates are formed through dissociation of NH3BH3. We also found that the dimerization of the NH3BH3 molecules to form c-(NH2BH2)2 is slightly exothermic, with an unexpected transition state that leads to the simultaneous release of two H2 molecules. The dehydrogenations of the oligomers are also exothermic, typically by less than 10 kcal/(mol of H2), with the largest exothermicity for n=3. The transition state search shows that the one-step direct dehydrocoupling cyclization of the oligomers is not a favored pathway because of high activation barriers. The dihydrogen bonding, in which protic (HN) hydrogens interact with hydridic (HB) hydrogens, plays a vital role in stabilizing different structures of the reactants, transition states, and products. The dihydrogen interaction (DHI) within the -BH2(η2-H2) moiety accounts for both the formation mechanisms of the oligomers and for the dehydrogenation of ammonia borane. Support was provided from the U.S. Department of Energy, Office of Basic Energy Sciences, Chemical Sciences Division and from the U.S. Department of Energy, Energy Efficiency and Renewable Energy, Chemical Hydrogen Storage Center of Excellence. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2010. "Fast-regenerable sulfur dioxide absorbents for lean-burn diesel engine emission control." Applied Catalysis. B, Environmental 100(1-2):238-244. Abstract It is known that sulfur oxides contribute significantly and deleteriously to the overall performance of lean-burn diesel engine aftertreatment systems, especially in the case of NOx traps. A Ag-based, fast regenerable SO2 absorbent has been developed and will be described. Over a temperature range of 300oC to 550oC, it absorbs almost all of the SO2 in the simulated exhaust gases during the lean cycles and can be fully regenerated by the short rich cycles at the same temperature. Its composition has been optimized as 1 wt% Pt-5wt%Ag-SiO2, and the preferred silica source for the supporting material has been identified as inert Cabosil fumed silica. The thermal instability of Ag2O under fuel-lean conditions at 230oC and above makes it possible to fast regenerate the sulfur-loaded absorbent during the following fuel-rich cycles. Pt catalyst helps reducing Ag2SO4 during rich cycles at low temperatures. And the chemically inert fumed SiO2 support gives the absorbent long term stability. This absorbent shows great potential to work under the same lean-rich cycling conditions as those imposed on the NOx traps, and thus, can protect the downstream particulate filter and the NOx trap from sulfur poisoning.
2010. "Molecular Structures and Energetics of the (ZrO₂)n and (HfO₂)n (n = 1-4) Clusters andTheir Anions." Journal of Physical Chemistry A 114(7):2665-2683. doi:10.1021/jp910310j Abstract The group IVB transition-metal dioxide clusters and their anions, (MO₂)n and (MO₂)n⁻ (M = Zr, Hf; n = 1-4), are studied with coupled cluster (CCSD(T)) theory and density functional theory (DFT). Similar to the results for M = Ti, these oxide clusters have a number of low-lying isomeric structures, which can make it difficult to predict the ground electronic state especially for the anion. Electron affinities for the low-lying structures are calculated and compared with those for M = Ti. Electron affinities of these clusters depend strongly on the cluster structures. Anion photoelectron spectra are calculated for the monomer and dimer and demonstrate the possibility for structural identification at a spectral line width of ≤0.05 eV. Electron excitation energies from the low-lying states to the singlet and triplet excited states are calculated self-consistently, as well as by the time-dependent DFT and equation-of-motion coupled cluster (EOM-CCSD) methods. The calculated excitation energies are compared to the band energies of bulk oxides, indicating that the excitation energy is not yet converged for n = 4 for these clusters. The excitation energies of the low-lying isomeric clusters are less than the bulk metal oxide band gaps and suggest that these clusters could be useful photocatalysts with a visible light source.
2010. "Synthesis and luminescence of CePO4:Tb/LaPO4 core/sheath nanowires." Nanotechnology 21(12):125604. Abstract CePO4:Tb/LaPO4 core/sheath architectured nanowires have been successful synthesized by a facile aqueous chemical method mediated by original CePO4:Tb aggregation seeds. The seed crystals serve as both a luminescence center and nucleation site for epitaxial growth. The seed nanocrystals have irregular sphere-like shape with an average size of around 6.8 nm and a narrow size distribution. When the seed crystals are coated with LaPO4, the resulting CePO4:Tb/LaPO4 core/sheath architectured nanowires have mean diameters of about 7.6 nm and lengths up to 331 nm. Both the photo- and X-ray luminescence demonstrate that the LaPO4 coating increases the luminescence efficiency. These core-sheath structured nanowires may find potential applications in solid state lighting, medical imaging and radiation detection.
2010. "Mechanical behavior of twinned SiC nanowires under combined tension-torsion and compression-torsion strain." Journal of Applied Physics 108(1):Art. No. 013504. doi:10.1063/1.3456002 Abstract The mechanical behavior of twinned silicon carbide (SiC) nanowires under combined tension-torsion and compression-torsion is investigated using molecular dynamics simulations with an empirical potential. The simulation results show that both the tensile failure stress and buckling stress decrease under combined tension-torsional and combined compression-torsional strain, and they decrease with increasing torsional rate under combined loading. The torsion rate has no effect on the elastic properties of the twinned SiC nanowires. The collapse of the twinned nanowires takes place in a twin stacking fault of the nanowires.
2010. "Direct Electrochemistry and Electrocatalysis of Myoglobin Immobilized on Graphene-CTAB-Ionic Liquid Nanocomposite Film." Electroanalysis 22(19):2297–2302. doi:10.1002/elan.201000044 Abstract We have investigated direct electrochemistry and electrocatalysis of myoglobin immobilized on graphene-cetylramethylammonium bromide (CTAB)-ionic liquid nanocomposite film on a glassy carbon electrode. The nanocomposite was characterized by TEM, SEM, XPS, and electrochemistry. It was found that the high surface area of graphene was helpful for immobilizing more proteins and the nanocomposite film can provide a favorable microenvironment for MB to retain its native structure and activity and to achieve reversible direct electron transfer reaction at an electrode. The nanocomposite films also exhibit good stability and catalytic activities for the electrocatalytic reduction of H2O2.
2010. "Numerical studies of three-dimensional stochastic Darcy's equation and stochastic advection-diffusion-dispersion equation." Journal of Scientific Computing 43(1):92-117. doi:10.1007/s10915-010-9346-5 Abstract In this study, we solve the three-dimensional stochastic Darcy's equation and stochastic advection-diffusion-dispersion equation using a probabilistic collocation method (PCM) on sparse grids. Karhunen-Lo\`{e}ve (KL) decomposition is employed to represent the three-dimensional log hydraulic conductivity $Y=\ln K_s$. The numerical examples which demonstrate the convergence of PCM are presented. It appears that the faster convergence rate in the variance can be obtained by using the Jacobi-chaos representing the truncated Gaussian distributions than using the Hermite-chaos for the Gaussian distribution. The effect of dispersion coefficient on the mean and standard deviation of the hydraulic head and solute concentration is investigated. Additionally, we also study how the statistical properties of the hydraulic head and solute concentration vary while using different types of random distributions and different standard deviations of random hydraulic conductivity.
2010. "Water-induced Formation of Cobalt Oxides Over Supported Cobalt/Ceria-Zirconia Catalysts under Ethanol-Steam Conditions." Journal of Catalysis 273(2):229-235. doi:10.1016/j.jcat.2010.05.016 Abstract The formation of water-induced cobalt oxides by re-oxidizing the metallic cobalt in the pre-reduced 10% Co/CeO2-ZrO2 catalyst was verified by in-situ TPR and in-situ XPS studies under various ethanol-steam conditions. The formation and transformation of water-induced cobalt oxide species were affected by the pre-reduction conditions used for the catalysts and the feed stream composition used in the reaction. This result suggests that the surface composition of the cobalt species in 10% Co-CZ catalyst, initially governed by the catalyst pre-treatment, was changed toward an equilibrium state that governed by the feed stream composition as the reaction proceeds. In addition, the reducibility of the ceria sites may play a significant role in the redox process involved both cobalt and ceria sites under ethanol-steam environment. Finally, the effect of the water-induced cobalt oxides on the catalytic performance, in particular for the carbon-carbon bond cleavage of ethanol, is negligible. However, these water-induced oxides may show importance for the subsequent reaction steps that determine the product selectivity during ethanol steam reforming, as their coexistence with the metallic cobalt species was revealed by the in-situ study under ethanol-steam conditions.
2010. "Uranium(VI) Diffusion in Low-Permeability Subsurface Materials." Radiochimica Acta 98(9-11):719-726. doi:10.1524/ract.2010.1773 Abstract Uranium(VI) diffusion was investigated in a fine-grained saprolite sediment that was collected from U.S. Department of Energy (DOE) Oak Ridge site, TN, where uranium contamination in groundwater is a major environmental concern. U(VI) diffusion was studied in a diffusion cell with one cell end in contact with a large, air-equilibrated electrolyte reservoir. The pH, carbonate and U(VI) concentrations in the reservoir solution were varied to investigate the effect of solution chemical composition and uranyl speciation on U(VI) diffusion. The rates of U(VI) diffusion were evaluated by monitoring the U(VI) concentration in the reservoir solution as a function of time; and by measuring the total concentration of U(VI) extracted from the sediment as a function of time and distance in the diffusion cells. The estimated apparent rate of U(VI) diffusion varied significantly with pH with the slowest rate observed at pH 7 as a result of strong adsorptive retardation. The estimated retardation factor was generally consistent with a surface complexation model. Numerical simulations indicated that a species-based diffusion model that incorporated both aqueous and surface complexation reactions was required to describe U(VI) diffusion in the low permeability material under variable geochemical conditions. Our results implied that low permeability materials will play an important role in storing U(VI) and attenuating U(VI) plume migration at circumneutral pH conditions, and will serve as a long-term source for releasing U(VI) back to the nearby aquifer during and after aquifer decontamination.
2010. "Site-Specific Proteomics Approach for Study Protein S-Nitrosylation." Analytical Chemistry 82(17):7160-7168. doi:10.1021/ac100569d Abstract Here we present a novel and robust method for the identification of protein S-nitrosylation sites in complex protein mixtures. The approach utilizes the cysteinyl affinity resin to selectively enrich S-nitrosylated peptides reduced by ascorbate followed by nanoscale liquid chromatography tandem mass spectrometry. Two alkylation agents with different added masses were employed to differentiate the S-nitrosylation sites from the non-Snitrosylation sites. We applied this approach to MDA-MB-231 cells treated with Angeli’s salt, a nitric oxide donor that has been shown to inhibit breast tumor growth and angiogenesis. A total of 162 S-nitrosylation sites were identified and an S-nitrosylation motif was revealed in our study. The 162 sites are significantly more than the number reported by previous methods, demonstrating the efficiency of our approach. Our approach will further facilitate the functional study of protein S-nitrosylation in cellular processes and may reveal new therapeutic targets.
2010. "Chromium-Assisted Synthesis of Platinum Nanocube Electrocatalysts." Chemical Communications 46(38):7184-7186. doi:10.1039/c0cc01379j Abstract This report describes a novel strategy of chromium-assisted shape control in the synthesis of platinum nanocubes with high monodispersity. The use of a certain concentration ratio of platinum vs. chromium precursors (typically 1:1) has been demonstrated to enable an effective adsorption of Cr species on the nanocrystal in selective blocking of the adsorption of capping molecules on the different surfaces for the nanocube formation. The cubic shape was evidenced by both high-resolution TEM and x-ray diffraction characterizations, whereas the composition was analyzed by both bulk and surfacesensitive techniques (DCP-AES, EDS and XPS). The results indicated that practically there was no Cr in the nanocubes or only a trace of Cr on the nanocrystal surfaces, demonstrating a high effectiveness in producing Pt nanocubes. A combination of effective oxidative leaving of the adsorbed Cr species and the weaker adsorption of capping molecules on Pt(111) constitutes the kinetic driving force for a faster growth rate of Pt(111) than Pt(100) faces. The understanding of the synergistic correlation between surface metal adsorption and ligand encapsulation in creating a difference in the kinetic growth on different nanocrystal facets has important implication to the design of advanced catalysts.
2010. "A Top-Down LC-FTICR MS-Based Strategy for Characterizing Oxidized Calmodulin in Activated Macrophages ." Journal of the American Society for Mass Spectrometry 21(6):930-939. Abstract Liquid chromatography-mass spectrometry (LC-MS) based approach for monitoring time dependent changes in the degree of nitration and oxidation of intact calmodulin (CaM) has been used to resolve approximately 500 CaM oxiforms. Tentative identifications of posttranslational modifications (PTMs) such as oxidation or nitration have been assigned by combining tryptic peptide information (generated from bottom-up analyses) with online collision induced dissociation (CID) tandem mass spectrometry (MS/MS) at the intact protein level. The reduction in abundance and diversity of oxidatively modified CaM (i.e. nitrated tyrosines and oxidized methionines) induced by macrophage activation has been explored and semi-quantified for different oxidation degrees of CaM (i.e. no oxidation, moderate and high oxidation). This work demonstrates the power of top-down approach to identify hundreds of combinations of posttranslational modifications (PTMs) for single protein target such as CaM.
2010. "Hydrogen Release Studies of Alkali Metal Amidoboranes." Inorganic Chemistry 49(8):3905-3910. Abstract A series of metal amido boranes LiNH2BH3 (LAB), NaNH2BH3 (SAB), LiNH(Me)BH3 (LMAB), NaNH(Me)BH3 (SMAB), KNH(Me)BH3 (PMAB), and KNH(tBu)BH3 (PBAB) were synthesized, by solution phase methods, and the thermal release of H2 in the solid state was studied. Based on the observed trends in reaction rates of H > Me > tBu and the kinetic isotope effect, the mechanism of hydrogen release from MAB compounds was found to proceed through a bimolecular mechanism involving the intermediacy of a MH (M = Li, Na, or K). The mechanism of hydrogen release from metal amidoboranes, a metal ion assisted hydride transfer, is very different than the mechanism of hydrogen release from the parent compound ammonia borane (AB). The non-volatile products formed from MAB’s are significantly different than the products formed after hydrogen release from AB. The boron containing resulting from the release of one equivalent of hydrogen from the metal amidoboranes were characterized by MAS 11B NMR spectroscopy and found to contain both BH3 and sp2 hybridized BH groups, consistent with a general structural feature MN(R)=BHN(R)MBH3. This work was funded by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy as part of the Chemical Hydrogen Storage CoE at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the U.S. DOE by Battelle. MAS NMR studies were performed using EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL.
2010. "Adsorption States and Mobility of TMAA Molecules on Reduced TiO2(110) Surface." Physical Chemistry Chemical Physics. PCCP 12(23):5986-5992. Abstract Combined scanning tunneling microscopy (STM), x-rays photoelectron spectroscopy (XPS) and density functional theory (DFT) studies have probed the bonding configurations and mobility of trimethylacetic acid (TMAA) molecules on TiO2(100) surface at RT. Upon TMAA dissociation through deprotonation, two distinctly different types of stable chemisorption configurations of the carboxylate group (TMA) have been identified accordingly to their position and appearance in STM images. In configuration A, two carboxylate O atoms bonds to two Ti4+ cations, while in configuration B one O atom fills the bridging oxygen vacancy (VO) with the other O bounded at an adjacent regular Ti4+ site. Calculated adsorption energies for the configurations A and B are comparable at 1.28 and 1.36 eV, respectively. DFT results also show that TMA may rotate at RT about its O atom that filled the VO (in configuration B), with a rotation barrier of ~0.65 eV. Both the observation of the constant initial sticking coefficient and preference for TMAA molecules to dissociate at selective sites indicate that TMAA adsorption is mediated by a mobile precursor state. Several possible molecular (physisorbed) states of TMAA have indeed been identified by DFT, all being a highly mobile at RT. In contrast, the TMA diffusion in chemisorbed (dissociative) state is a very slow with calculated barrier of 1.09 eV for diffusion along the Ti row.
