Scientific Publications 2008
2008. "PdZnAl Catalysts for the Reactions of Water-Gas-Shift, Methanol Steam Reforming, and Reverse-Water-Gas-Shift." Applied Catalysis. A, General 342(1-2):63-68. doi:10.1016/j.apcata.2008.03.005 Abstract Pd/ZnO/Al2O3 catalysts were studied for water-gas-shift (WGS), methanol steam reforming, and reverse-water-gas-shift (RWGS) reactions. WGS activity was found to be dependent on the Pd:Zn ratio with a maximum activity obtained at approximately 0.50, which was comparable to that of a commercial Pt-based catalyst. The catalyst stability was demonstrated for 100 hours time-on-stream at a temperature of 3600C without evidence of metal sintering. WGS reaction rates were approximately 1st order with respect to CO concentration, and kinetic parameters were determined to be Ea = 58.3 kJ mol-1 and k0 = 6.1x107 min-1. During methanol steam reforming, the CO selectivities were observed to be lower than the calculated equilibrium values over a range of temperatures and steam/carbon ratios studied while the reaction rate constants were approximately of the same magnitude for both WGS and methanol steam reforming. These results indicate that although Pd/ZnO/Al2O3 are active WGS catalysts, WGS is not involved in methanol steam reforming. RWGS rate constants are on the order of about 20 times lower than that of methanol steam reforming, suggesting that RWGS reaction could be one of the sources for small amount of CO formation in methanol steam reforming.
2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7(3):1209-1217. doi:10.1021/pr070441i Abstract Comparing a protein’s concentrations across two or more treatments is the focus of many proteomics studies. A frequent source of measurements for these comparisons is a mass spectrometry (MS) analysis of a protein’s peptide ions separated by liquid chromatography (LC) following its enzymatic digestion. Alas, LC-MS identification and quantification of equimolar peptides can vary significantly due to their unequal digestion, separation and ionization. This unequal measurability of peptides, the largest source of LC-MS nuisance variation, stymies confident comparison of a protein’s concentration across treatments. Our objective is to introduce a mixed-effects statistical model for comparative LC-MS proteomics studies. We describe LC-MS peptide abundance with a linear model featuring pivotal terms that account for unequal peptide LC-MS measurability. We advance fitting this model to an often incomplete LC-MS dataset with REstricted Maximum Likelihood (REML) estimation, producing estimates of model goodness-offit, treatment effects, standard errors, confidence intervals, and protein relative concentrations. We illustrate the model with an experiment featuring a known dilution series of a filamentous ascomycete fungus Trichoderma reesei protein mixture. For the 781 of 1546 T.reesei proteins with sufficient data coverage, the fitted mixed-effects models capably described the LC-MS measurements. The LC-MS measurability terms effectively accounted for this major source of uncertainty. Ninety percent of the relative concentration estimates were within 1/2 fold of the true relative concentrations. Akin to the common ratio method, this model also produced biased estimates, albeit less biased. Bias decreased significantly, both absolutely and relative to the ratio method, as the number of observed peptides per protein increased. Mixed-effects statistical modeling offers a flexible, well-established methodology for comparative proteomics studies integrating common experimental designs with LC-MS sample processing plans. It favorably accounts for the unequal LC-MS measurability of peptides and produces informative quantitative comparisons of a protein’s concentration across treatments with objective measures of uncertainties.
2008. "Fully Relativistic Calculations on the Potential Energy Surfaces of the Lowest 23 States of Molecular Chlorine." Journal of Chemical Physics 128(4):Art. No. 041101. doi:10.1063/1.2827457 Abstract The electronic structure and spectroscopic properties (Re, ωeϰe, βe, Te ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.
2008. "Correlation of Calculated Excited-state Energies and Experimental Quantum Yields of Luminescent Tb(III) β-diketonates." Journal of Physical Chemistry A 112(20):4527-4530. doi:10.1021/jp8002799 Abstract Theoretical calculations employing time dependent density functional theory (TDDFT) are used to characterize the excited states of Tb(III) β-diketonate complexes. Calculated results are compared directly with experimental results that together show a correlation between relative quantum yields and the excited-state energies that depend on the electronic properties of the p,p’- substituent group associated with the coordinating N-donor neutral ligand. It is found that changes in the electron donating nature of the neutral ligand structure leads to shifts in the lowest triplet energy level of the complex that consequently changes the relative quantum yield. Thus providing critical direction for the synthesis of high quantum yield terbium complexes.
2008. "Dynamic annealing of defects in irradiated zirconia-based ceramics." Journal of Materials Research 23(3):593-597. doi:10.1557/JMR.2008.0104 Abstract We have observed self-healing behavior in large scale molecular dynamics simulations of 30 keV Zr recoils in pure zirconia and 10 mole % yttria-stabilized zirconia. Our results reveal that dynamic annealing is highly effective during the first 5 ps of damage evolution, especially in the presence of oxygen structural vacancies introduced by aliovalent doping (Y3+ substitution for Zr4+). The presence of mobile oxygen vacancies results in near complete recovery of damage. Damage recovery on the cation sublattice is assisted by the anion sublattice recovery, which explains the remarkable radiation tolerance of stabilized zirconia. Ceramics engineered to heal themselves in this fashion hold great promise for use in high-radiation environments or for safely encapsulating high-level radioactive waste over geological time scales.
2008. "Thermodynamic and Structural Features of Aqueous Ce(III)." Journal of Physical Chemistry A 112(44):11198–11206. doi:10.1021/jp8076408 Abstract With a single f-electron, Ce(III) is the simplest test case for benchmarking the thermodynamic and structural properties of hydrated Ln(III) against varying density functionals and reaction field models, in addition to determining the importance of multiconfigurational character in their wave functions. Here, the electronic structure of Ce(H₂O)x(H₂O)y 3+ (x =8, 9; y= 0, 12-14) has been examined using DFT and CASSCF calculations. The latter confirmed that the wave function of octa- and nona-aqua Ce(III) is well-described by a single configuration. Benchmarking was performed for density functionals, reaction field cavity types, and solvation reactions against the experimental free energy of hydration, ΔGhyd(Ce3+). The UA0, UAKS, Pauling, and UFF polarized continuum model cavities displayed different performance, depending on whether one or two hydration shells were examined, and as a function of the size of the metal basis set. These results were essentially independent of the density functional employed. Using these benchmarks, the free energy for water exchange between CN = 8 and CN = 9, for which no experimental data are available, was estimated to be approximately -4 kcal/mol.
2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Journal of Chromatography B 871(2):243-252. doi:10.1016/j.jchromb.2008.04.040 Abstract We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput quantitative LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. In addition, we also report on the optimization of a reversed-phase LC method for the separation of lipids in these sample types.
2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹⁸O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24. doi:10.1021/pr7007785 Abstract Reversible protein phosphorylation is a central cellular regulatory mechanism in modulating protein activity and propagating signals within cellular pathways and networks. Development of more effective methods for the simultaneous identification of phosphorylation sites and quantification of temporal changes in protein phosphorylation could provide important insights into molecular signaling mechanisms in a variety of different cellular processes. Here we present an integrated quantitative phosphoproteomics approach and its applications for comparative analysis of Cos-7 cells in response to lysophosphatidic acid (LPA) gradient stimulation. The approach combines trypsin-catalyzed 16O/18O labeling plus 16O/18O-methanol esterification labeling for quantitation, a macro- Immobilized Metal-ion Affinity Chromatography trap for phosphopeptide enrichment, and a monolithic capillary column with integrated electrospray emitter. LC separation and MS/MS is followed by neutral loss-dependent MS/MS/MS for phosphopeptide identification using a linear ion trap (LTQ)-FT mass spectrometer and complementary searching algorithms for interpreting MS/MS spectra. Protein phosphorylation involved in various signaling pathways of cell migration were identified and quantified, such as mitogen-activated protein kinase 1, dual-specificity mitogen-activated protein kinase kinase 2, and dual-specificity tyrosine-phosphorylation regulated kinase 1b, and a number of Rho GTPase-activating proteins. These results demonstrate the efficiency of this quantitative phosphoproteomics approach and its application for rapid discovery of phosphorylation events associated with gradient sensing and cell chemotaxis.
2008. "Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor." Biochimica et Biophysica Acta--Proteins and Proteomics 1784(12):1935-1941. doi:10.1016/j.bbapap.2008.06.011 Abstract e(III) oxides are the most abundant source of reducible Fe(III) by microorganisms in most soils and sediments, yet few studies on the physiology of Fe(III)-reducing microorganisms during growth on Fe(III) oxide have been conducted because of the technical difficulties in working with cell growth and harvest in the presence of Fe(III) oxides. Geobacter sulfurreducens is a representative of the Geobacter species that predominate in a variety of subsurface environments in which Fe(III) oxide is important. In order to better understand the physiology of Geobacter species during growth on Fe(III) oxide, the proteome of G. sulfurreducens grown on Fe(III) oxide was compared with the proteome of cells grown with soluble Fe(III) citrate. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) revealed 19 proteins that were more abundant during growth on Fe(III) oxide than on soluble Fe(III). These included proteins related to protein synthesis, electron transfer and energy production, oxidative stress, protein folding, outer membrane proteins, nitrogen metabolism and hypothetical proteins. Further analysis of the proteome with the accurate mass and time (AMT) tag method revealed additional proteins associated with growth on Fe(III) oxide. These included the outer-membrane c-type cytochrome, OmcS and OmcG, which genetic studies have suggested are required for Fe(III) oxide reduction. Furthermore, several other cytochromes, as yet unstudied, were detected to be significantly up regulated during growth on Fe(III) oxide and other proteins of unknown function were more abundant during growth on Fe(III) oxide than on soluble Fe(III). PilA, the structural protein for pili, which is required for Fe(III) oxide reduction, and other pilin-associated proteins were also more abundant during growth on Fe(III) oxide. Confirmation of the differential expression of proteins known to be important in Fe(III) oxide reduction was observed, and an additional number of previously unidentified proteins were found with significant abundance in the cells grown under conditions of Fe(III) oxide reduction.
2008. "Structure and Heats of Formation of Iodine Fluorides and theRespective Closed-Shell Ions from CCSD(T) Electronic StructureCalculations and Reliable Prediction of the Steric Activity of theFree-Valence Electron Pair in ClF₆⁻, BrF₆⁻, and IF₆⁻." Inorganic Chemistry 47(12):5485-5494. doi:10.1021/ic800021h Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for IF, IF₂-, IF₂+, IF₃, IF₄-, IF₄+,IF₅, IF₆-, IF₆+, IF₇, IF₈-, BrF₆-, and ClF₆- from coupled cluster theory [CCSD(T)] calculations with effective-core potential correlation-consistent basis sets for I. In order to achieve near chemical accuracy (±1 kcal/mol), three corrections were added to the complete basis set binding energies based on frozen-core coupled-cluster theory energies: a correction for core-valence effects, a correction for scalar relativistic effects, and a correction for firstorder atomic spin-orbit effects. Vibrational zero-point energies were computed at the coupled-cluster level of theory except for IF₆-, IF₇, and IF₈-. The calculated heats of formation for the neutral and ionic IFn fluorides were used to predict fluoride affinities. It is shown that high-level calculations are required to predict correctly the steric activity of the free-valence electron pair on the central atoms in IF₆- (C₃v), BrF₆- (Oh), and ClF₆- (Oh). The vibrational spectrum of IF₈- was reanalyzed, and complete mode descriptions for square-antiprismatic XF₈ species of D₄d symmetry are given.
2008. "Understanding How Surface Morphology and Hydrogen Dissolution Influence Ethylene Hydrogenation on Palladium." Journal of Physical Chemistry C 112(40):15796-15801. doi:10.1021/jp803880x Abstract Ethylene hydrogenation is a prototypical reaction for catalytic hydrogenation of unsaturated hydrocarbons and as such it has been studied on a number of metals. On single crystalline Pd(111), Pd(110), and Pd(100) surfaces this reaction has been shown to be structure insensitive and to occur with extremely low yield (0.1%) (refs). Recent studies on support4ed Pd particles showed an approximately 10-folded increase in the ethane yield per surface Pd atom which was attributed to the increased surface to bulk Pd ratio on the particles thereby giving rise to reduced sorption of hydrogen into the bulk. The enhanced concentration of surface hydrogen is believed to result in the observed increase in catalytic activity. Even on these nanoparticles the C2H6 yield is relatively low (~2%)(refs).
2008. "Sulfur Isotopes as Indicators of Amended Bacterial Sulfate Reduction Processes Influencing Field Scale Uranium Bioremediation." Environmental Science & Technology 42(21):7842-7849. doi:10.1021/es800414s Abstract Aqueous uranium (U(VI)) concentrations in a contaminated aquifer in Rifle Colorado have been successfully lowered through electron donor amended bioreduction. Samples collected during the acetate amendment experiment were analyzed for aqueous concentrations of Fe(II), sulfate, sulfide, acetate, U(VI), and δ34S of sulfate and sulfide to explore the utility of sulfur isotopes as indicators of in situ acetate amended sulfate and uranium bioreduction processes. Enrichment of up to 7‰ in δ34S of sulfate in down-gradient monitoring wells indicates a transition to elevated bacterial sulfate reduction. A depletion in Fe(II), sulfate, and sulfide concentrations at the height of sulfate reduction, along with an increase in the δ34S of sulfide to levels approaching the d34S values of sulfate, indicates sulfate limited conditions concurrent with a rebound in U(VI) concentrations. Upon cessation of acetate amendment, sulfate and sulfide concentrations increased, while δ34S values of sulfide returned to less than -20‰ and sulfate δ34S decreased to near-background values, indicating lower levels of sulfate reduction accompanied by a corresponding drop in U(VI). Results indicate a transition between electron donor and sulfate-limited conditions at the height of sulfate reduction and suggest stability of biogenic FeS precipitates following the end of acetate amendment.
2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7(7):2595-2604. doi:10.1021/pr0704837 Abstract Motivation: Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still re-main related to how best to extract biological information from dy-namic proteomics data; for example, challenges related to extrane-ous variability, missing abundance values, and the identification of significant temporal patterns. Results: This article describes a strategy that addresses the afore-mentioned issues for the analysis of temporal bottom-up proteomics data. The core strategy for the data analysis algorithms and subse-quent data interpretation was formulated to take advantage of the temporal properties of the data. The analysis procedure presented herein was applied to data from a Rhodobacter sphaeroides 2.4.1 time-course study. The results were in close agreement with existing knowledge about R. sphaeroides, therefore demonstrating the utility of this analytical strategy.
2008. "Transient Mobility of Oxygen Adatoms upon O2 Dissociation on Reduced TiO2 (110)." Journal of Physical Chemistry C 112(7):2649-2653. doi:10.1021/jp077677u Abstract Tracking the same region of the reduced TiO2 (110) surface by scanning tunneling microscopy before and after oxygen exposure at room temperature confirms that O2 molecules dissociate only at the bridging oxygen vacancies, with one O atom healing a vacancy and other O atom bonding at the neighboring Ti site as an adatom. Majority (~81%) of O adatoms are found separated from the original vacancy positions, by up to two lattice constants along  direction. Since at room temperature the thermal diffusion of O adatoms has been found to be rather small, with experimentally estimated activation energy of ~1.1 eV, we conclude that observed lateral distribution of the oxygen adatoms is attained through a nonthermal, transient mobility in the course of O2 dissociation. Unlike for other known cases of the dissociation of the diatomic molecules where both “hot” adatoms accommodate at the equivalent sites, in the studied system the oxygen atoms filling the vacancies are locked into the bridging oxygen rows and only the O adatoms are relatively free to move. The transient motion of the hyperthermal oxygen adatoms on the TiO2 (110) surface occurs exclusively along the Ti troughs.
2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82(13):6524-6535. doi:doi:10.1128/JVI.00502-08 Abstract Human cytomegalovirus (HCMV) is implicated in the acceleration of a number of vascular diseases including transplant vascular sclerosis (TVS), the lesion associated with chronic rejection (CR) of solid organ transplants. Although the virus persists in the allograft throughout the course of disease, few cells are directly infected by CMV. This observation is in contrast to the global effects that CMV has on the acceleration of TVS/CR, suggesting that CMV infection indirectly promotes the vascular disease process. Recent transcriptome analysis of CMV-infected heart allografts indicates that the virus induces cytokines and growth factors associated with angiogenesis (AG) and wound healing (WH), suggesting that CMV may accelerate TVS/CR through the induction and secretion of AG/WH factors from infected cells. We analyzed virus-free supernatants from HCMV-infected cells (HCMV secretomes) for growth factors, by mass spectrometry and immunoassays, and found that the HCMV secretome contains over 1,000 cellular proteins, many of which are involved in AG/WH. Importantly, functional assays demonstrated that CMV but not herpes simplex virus secretomes not only induce AG/WH but also promote neovessel stabilization and endothelial cell survival for 2 weeks. These findings suggest that CMV acceleration of TVS occurs through virus-induced growth factors and cytokines in the CMV secretome.