Scientific Publications 2008
2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3(2):e1542. doi:10.1371/journal.pone.0001542 Abstract Comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry. Experimental validation of the existence of this core genome requires extensive measurement and is not typically undertaken. Enabled by an extensive proteome database development over a six year period, we experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. While genomic studies establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.
2008. "Self-assembled nanostructures from homopolymer induced by UV and solvent exposure." Soft Matter 4:2164-2167. doi:10.1039/b807328g Abstract A simple method for creating self-assembled nanostructures using a single polymer system is reported. When spin-coated polystyrene thin films were irradiated with UV light and treated with toluene, unique nanostructures were observed, evolving from star-shaped networks to arrays of concentric circles. The nanostructure formation is a result of differential responses of crosslinked and oxidized products to the solvent by a combined effect of phase separation and solvent swelling. The nanostructures were observed for polymers of different molecular weights, films of different thicknesses, and on various substrates.
2008. "Superior Nanoscale Passive Oxide Layers Synthesized Under Photon Irradiation for Environmental Protection." Applied Physics Letters 92(26):263103. doi:10.1063/1.2952282 Abstract We report on synthesis and functional properties of ultra-thin oxide layers synthesized on metal surfaces by room temperature photon irradiation. We show that the impedance of a passive aluminum oxide film synthesized under ultraviolet photon irradiation is an order of magnitude larger than that of native oxide in a 0.5 M NaCl solution. Further, the structure and impedance of existing native oxide layers can be dramatically improved by minutes-long exposure to photon-irradiation. Depth profiling studies with X-ray photoelectron spectroscopy shows that chlorine uptake in UV-synthesized oxides, compared to that of native oxides, is reduced which can contribute to the improvement in corrosion resistance. The results are of significance to synthesis of ultra-thin passive layers on metal and alloy structures for environmental protection.
2008. "Thermal stability and oxidation resistance of TiCrAlYO coatings on SS430 for solid oxide fuel cell interconnect applications." Surface & Coatings Technology 202(19):4820-4824. doi:10.1016/j.surfcoat.2008.04.059 Abstract Chromia-forming ferritic stainless steels are being considered for interconnects applications in planar solid oxide fuel cell (SOFC) stacks because of their low cost and physical properties. At high temperatures, ferritic steels lack environmental stability in the SOFC operating environment, and gradually degrade the cell performance. In this study, an effective, dense and well adherent TiCrAlYO coating was deposited on an SS430 alloy using the filtered arc deposition technique. High-energy ion backscattering was used to characterize the composition and the thermal stability of the coatings. The chromium volatility of the coated steel plates at 800 oC was also measured using ion beam analysis. Significant reductions in oxidation rates as well as reduced Cr volatility were observed for the coated alloys.
2008. "Natural Oxidation of Black Carbon in Soils: Changes in Molecular Form and Surface Charge along a Climosequence." Geochimica et Cosmochimica Acta 72(6):1598-1610. Abstract The aim of this work was to investigate changes in molecular form and surface charge of black carbon (BC) due to longtermnatural oxidation and to examine how climatic and soil factors affect BC oxidation. Black C was collected from 11 historical charcoal blast furnace sites with a geographic distribution from Quebec, Canada, to Georgia, USA, and compared to BC that was newly produced (new BC) using rebuilt historical kilns. The results showed that the historical BC samples were substantially oxidized after 130 years in soils as compared to new BC or BC incubated for one year. The major alterations by natural oxidation of BC included: (1) changes in elemental composition with increases in oxygen (O) from 7.2% in new BC to 24.8% in historical BC and decreases in C from 90.8% to 70.5%; (2) formation of oxygen-containing functional groups, particularly carboxylic and phenolic functional groups, and (3) disappearance of surface positive charge and evolution of surface negative charge after 12 months of incubation. Although time of exposure significantly increased natural oxidation of BC, a significant positive relationship between mean annual temperature (MAT) and BC oxidation (O/C ratio with r = 0.83;P < 0.01) explained that BC oxidation was increased by 87 mmole kg Cˉ1 per unit Celsius increase in MAT. This long-term oxidation was more pronounced on BC surfaces than for entire particles, and responded 7-fold stronger to increases in MAT. Our results also indicated that oxidation of BC was more important than adsorption of non-BC. Thus, natural oxidation of BC may play an important role in the effects of BC on soil biogeochemistry.
2008. "Stability of black carbon in soils across a climatic gradient." Journal of Geophysical Research. Biogeosciences 113(G2):Art. No. G02027. Abstract The recalcitrant properties of black carbon (BC) grant it to be a significant pool of stable C in soils. Up to now, however, the longevity of BC under different climates is still unclear. In this study, we used BC samples from historical charcoal blast furnace sites to examine the stability of BC across a climatic gradient of mean annual temperatures (MAT) from 3.9 to 17.2ºC. The results showed that C concentration and C storage in the BC-containing soils at a soil depth of 0 - 0.2 m were 9.0 and 4.7 times higher than those in adjacent soils, respectively. Carbon in the BC-containing soils was more stable, with a significantly lower amount of labile C fraction (4.4 mg g C-1 vs. 27.5 mg g C-1) and longer half-life of the recalcitrant C fraction (59 years vs. 9 years) than the adjacent soils determined from incubation experiments. The stability of BC was primarily due to its inherently recalcitrant chemical composition as suggested by short-term incubation and solid state 13C nuclear magnetic resonance spectra of isolated BC particles. A significant negative relationship between C storage and MAT (-0.62; P<0.01) further indicated that C storage was decreased with warmer climate. However, the lack of a relationship between MAT and BC mineralization (P>0.05) suggested that the stability of the remaining BC was similar between sites with very different MAT. Despite the fact that warming or cooling result in immediate consequences for BC stocks, it may have little impact on the stability of the remaining BC over the period studied.
2008. "Effect of BaO Morphology on NOx Abatement: NO₂ Interaction with Unsupported and γ-Al₂O₃-Supported BaO." Journal of Physical Chemistry C 112(43):16924–16931. doi:10.1021/jp806884c Abstract First-principles density functional theory calculations have been applied to study NO₂ interaction with BaO in various morphologies, including extended BaO surfaces as well as unsupported and γ-Al₂O₃-supported BaO clusters. Adsorption of NO₂ over BaO of different morphologies studied with the same method allowed a direct comparison of adsorption structures and energetics. In comparison with the flat BaO(100) surface, the presence of the low-coordinated sites on the small BaO clusters and at the edge of the stepped BaO(310) surface not only strengthens the binding of NO₂ at these sites but also creates new NO₂ binding modes. The adsorption of NO₂ at the accessible edge oxygen sites on the BaO clusters and stepped BaO(310) surface led to the formation of a nitrate species with the new N-O (surface or cluster) bond length of 1.3-1.5 Å. Furthermore, BaO(310) created an adsorption configuration with two oxygen atoms of the adsorbed NO₂ bridging the step-edge and terrace Ba sites. This adsorption configuration has an adsorption energy of 1.39 eV and cannot be formed on BaO(100). The nonstoichiometric clusters and defective surfaces with either O or Ba vacancies exhibit much stronger affinity toward NO₂, up to 4.09 eV for NO₂ adsorption at the edge oxygen site of Ba14O13. NO2 prefers interacting with the nucleophilic substrate (O deficient) through its O atoms in an O-down configuration. Consequently, the adsorbed NO₂ molecule gains partial electronic charge from the substrate, forming a NO₂ δ- species. On the other hand, the NO₂ interacts with the electrophilic substrate (Ba deficient) by sharing its lone pair electrons on the N atom with a surface O site which resulted in a NO₃ δ- species. Furthermore, the synergistic effect of γ-Al2O3 and BaO toward NO₂ adsorption reported previously (Cheng, L.; Ge, Q. Surf. Sci. 2007, 601, L65) was confirmed with a larger γ-Al₂O₃ surface unit cell that isolates the supported BaO cluster from its periodic images. The synergistic effect was attributed to the enhanced basicity and acidity of the supported BaO cluster and the γ-Al₂O₃ surface, respectively.
2008. "Probing Emissions of Military Cargo Aircraft: Description of a Joint Field Measurement Strategic Environmental Research and Development Program." EM: Air & Waste Management Association's magazine for environmental managers 58(6):787-796. Abstract To develop effective air quality control strategies for military air bases, there is a need to accurately quantify these emissions. In support of the Strategic Environmental Research and Development Program project, the PM and gaseous emissions from two T56 engines on a parked C-130 aircraft were characterized at the Kentucky Air National Guard base in Louisville, KY. Conventional and research-grade instrumentation and methodology were employed in the field campaign during the first week of October 2005. Particulate emissions were sampled at the engine exit plane and at 15 meters downstream. In addition, remote sensing of the gaseous species was performed via spectroscopic techniques at 5 and 15 m downstream of the engine exit. It was found that PM mass and number concentrations measured at 15-m downstream locations, after dilution corrected, generally agreed well with those measured at the engine exhaust plane; however, higher variations were observed in the far-field after natural dilution of the downstream measurements was accounted for. Using CO2-normalized data we demonstrated that gas species measurements by extractive and remote sensing techniques agreed reasonably well.
2008. "NMR Studies of Cu/zeolite SCR Catalysts Hydrothermally Aged with Urea." Catalysis Today 136(1-2):34-39. doi:10.1016/j.cattod.2008.01.019 Abstract The effects of hydrothermal aging of Cu/zeolite urea-SCR catalysts on their reactivity and material properties was assessed by performance tests and multiple characterization techniques that included 27Al NMR and XRD. Three aging protocols were used that consisted of varying temperature during hydrothermal aging with or without exposure to aqueous urea solution. Differences in behavior were even found for samples hydrothermally aged immediately following exposure to the urea solution or if the sample was dried overnight before hydrothermal aging. The combination of urea and high temperature exposure increased the deactivation of Cu/zeolite SCR catalysts beyond that observed by hydrothermal aging alone, with an immediate high temperature exposure following wetting of the catalyst core with aqueous urea causing the most significant deterioration in performance. The impact of urea on SCR catalyst durability was also found to increase with the aging temperature. NMR analysis suggested that aging with urea resulted in relatively more dealumination of the zeolite for the SCR catalysts in this study.
2008. "N incorporation, composition and electronic structure in N-doped TiO2(001) anatase epitaxial films grown on LaAlO3(001)." Surface Science 602(1):133-141. doi:10.1016/j.susc.2007.09.061 Abstract We have investigated the properties of N-doped TiO2 anatase grown by plasma-assisted molecular beam epitaxy on LaAlO3(001) substrates. Phase-pure epitaxial films in which N substitutes for O with no secondary phases formation occur only over a narrow range of fluxes. The N solubility is limited to ~0.2 at. % of the anions and is an order of magnitude lower than that found in N-doped rutile. N substitution for O results in N 2p derived states off the top of the anatase valence band and the associated red shift in the optical bandgap.
2008. "Silicon Control of Strontium and Cesium Partitioning in Hydroxide-Weathered Sediments." Geochimica et Cosmochimica Acta 72(8):2024-2047. Abstract Cation partitioning in an aqueous soil suspension depends on the coupling of reaction time, sorbate amount and mineral weathering reactions. These factors were varied in sediment suspension experiments to identify geochemical processes that affect migration of Sr2+ and Cs+ introduced to the subsurface by caustic high level radioactive waste (HLRW). Three glacio-fluvial and lacustrine sediments from the Hanford Site were subjected to hyperalkaline (pH > 13), Na–Al–NO3–OH solution conditions within a gradient field of (i) sorptive concentration (10-5–10-3 M) and (ii) reaction time (0–365 d). Strontium uptake (qSr) exceeded that of cesium at nearly all reaction times. Sorbent affinity for both Cs+ and Sr2+ increased with clay plus silt content at early times, but a prolonged slow uptake process was observed over the course of sediment weathering that erased the texture effect for Sr2+; all sediments showed similar mass normalized uptake after several months of reaction time. Strontium became progressively recalcitrant to desorption after 92 d, with accumulation and aging of neoformed aluminosilicates. Formation of Cs+ and Sr2+-containing cancrinite and sodalite was observed after 183 d by SEM and synchrotron u-XRF and u-XRD. EXAFS data showed ncorporation of Sr2+ into both feldspathoid and SrCO3(s) coordination environments after one year. Adsorption was predominant at early times and low sorbate amount, whereas recipitation, controlled largely by sediment Si release, became increasingly important at longer times and higher sorbate amount. Kinetics of contaminant desorption at pH 8 from one year-weathered sediments showed significant dependence on background cation (Ca2+ versus K+) composition. Results of this study indicate that co-precipitation and ion exchange in neoformed aluminosilicates may be an important mechanism controlling Sr2+ and Cs+ mobility in siliceous sediments impacted by hyperalkaline HLRW.
2008. "Density Functional and Basis Set Dependence of Hydrated Ln(III) Properties." Journal of Chemical Theory and Computation 4(5):708-718. doi:10.1021/ct700317p Abstract Benchmark studies of Ln(H₂O)₁‚₈₋₉³⁺ (Ln ) La, Lu) have been performed to assess the calculated properties obtained with local density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid functionals, when used with small- and largecore relativistic effective core potentials and their associated bases. Basis set dependence and the importance of specific functions to adequately describe the Ln atomic orbitals have been determined. The lanthanide contraction has been found to be an insufficient metric for characterizing the quality of a method/basis set combination due to cancellation of the errors. The electrostatic description obtained by natural population analysis has been examined, and an alternative partitioning of the valence space, which includes the 6s6p5d4f natural atomic orbitals, has been proposed.
2008. "Allochromatium vinosum DsrC: Solution-State NMR Structure, Redox Properties and Interaction with DsrEFH, a Protein Essential for Purple Sulfur Bacterial Sulfur Oxidation ." Journal of Molecular Biology 382:692-707. doi:10.1016/j.jmb.2008.07.022 Abstract Sequenced genomes of dissimilatory sulfur-oxidizing and sulfate-reducing bacteria containing genes coding for DsrAB, the enzyme dissimilatory sulfite reductase, inevitably also contain the gene coding for the 12-kDa DsrC protein. DsrC is thought to have a yet unidentified role associated with the activity of DsrAB. Here we report the solution structure of DsrC from the sulfur-oxidizing purple sulfur bacterium Allochromatium vinosum determined with NMR spectroscopy in reducing conditions, and describe the redox behavior of two conserved cysteine residues upon transfer to an oxidizing environment. In reducing conditions, the DsrC structure is disordered in the highly conserved carboxy-terminus. We present multiple lines of evidence that in oxidizing conditions, a strictly conserved cysteine (Cys111) at the penultimate position in the sequence forms an intramolecular disulfide bond with Cys100, which is conserved in DsrC in all organisms with DsrAB. This intramolecularly disulfide-bonded species is the thermodynamically stable form of the protein in oxidizing conditions and forms after rapid formation of the kinetic product, an intermolecular Cys111-Cys111 disulfide-bonded dimer. Treatment of these forms with reducing agent regenerates the monomeric species that was structurally characterized. Furthermore, evidence is provided for strong and specific interaction of DsrC with heterohexameric DsrEFH, a protein encoded in the same operon. Mutation of Cys100 to serine prevented formation of the DsrC species assigned as an intramolecular disulfide in oxidizing conditions, while still allowing formation of the intermolecular Cys111-Cys111 dimer. In the reduced form this mutant protein still interacted with DsrEFH. This was not the case for the Cys111Ser and the Cys100Ser/Cys111Ser mutants, both of which also did not form protein dimers. Our observations highlight the central importance of the carboxy-terminal DsrC cysteine residues and would be consistent with a role as a sulfur-substrate binding/transferring protein as well as with an electron-transfer function via thiol-disulfide interchanges.
2008. "Structure of an Acetyl-CoA Binding Protein from Staphylococcus aureus Representing a Novel Subfamily of GCN5-related N-Acetyltransferase-like Proteins." Journal of Structural and Functional Genomics 9(1-4):7-20. doi:10.1007/s10969-008-9041-z Abstract We have determined the NMR structure of SACOL2532, a putative GCN5-like N-acetyltransferase (GNAT) from Staphylococcus aureus. SACOL2532 is structural genomics target ZR31 of the Northeast Structural Genomics Consortium. SACOL2532 was shown to bind both CoA and acetyl-CoA, and structures with and without bound CoA were determined. Following analysis of the structure and sequence, a subfamily of small GCN5-related N-acetyltransferase (GNAT)-like proteins can be defined. Proteins from this subfamily, which we designate C-GNAT for cysteine-containing GNAT, are characterized by a cysteine residue in the acetyl-CoA binding site near the acetyl group, by their small size in relation to other GNATs, by a lack of obvious substrate binding site, and by a distinct conformation of bound CoA in relation to other GNATs. Subfamily members are found in many bacterial and eukaryotic genomes, and in some archaeal genomes. Whereas other GNATs transfer the acetyl group of acetyl-CoA directly to an aliphatic amine, the presence of the conserved cysteine residue suggests that proteins in the C-GNAT subfamily transfer an acetyl group from acetyl-CoA to one or more presently unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The apparent absence of a substrate-binding region may suggest that the substrate is a macromolecule, such as another protein, or that a second protein subunit providing a substrate-binding region must combine with SACOL2532 to make a fully functional N-acetyl transferase.
2008. "An Investigation of the Rotamers of Butadiene by High-Resolution Infrared Spectroscopy." Journal of Physical Chemistry A 112(49):12637-12646. doi:10.1021/jp807677y Abstract A wide-ranging investigation of the high-resolution infrared spectrum of 1,3-butadiene was undertaken with the prime objective of finding subbands in the rotational structure attributable to the gauche rotamer, from which information about the molecular structure could be derived. The one band near 750 cm-1, which had previously been assigned to the gauche rotamer, has been shown to be a difference tone for the trans rotamer. Despite careful searching, no subbands attributable to the gauche rotamer have been found. Two weak Q branches at 463.82 and 462.19 cm-1 might arise from the gauche rotamer. The rotational structure, including two hot bands, was analyzed in the C-type band for the v12(au) mode near 525 cm-1 and the Ctype band near 162 cm-1 for the v13(au) mode. A rotational analysis was also done for the A-type band for the v24(bu) band near 300 cm-1. An unsuccessful attempt was made to extend the analysis of the B-type component of the A/B-type band for v17(bu) near 3000 cm-1. With the exception of the two weak Q branches near 460 cm-1, no new evidence for the gauche rotamer was found.
2008. "Stable Icosahedral Hollow Cage Clusters: Stannapherene (Sn12 2-) and Plumbaspherene (Pb12 2-)." International Reviews in Physical Chemistry 27(1):139-166. Abstract One of the major objectives of cluster science is to discover stable atomic clusters, which may be used as building blocks for cluster-assembled nanomaterials. The discovery and bulk synthesis of the fullerenes have sprouted new research disciplines in chemistry and nanoscience and precipitated intense interests to search for other similar stable clusters. However, despite major research efforts, no other analogous gas-phase clusters have been found and yielded to bulk syntheses. In this article, we review our recent discoveries in cluster beam experiments of stannaspherene (Sn12 2–) and plumbaspherene (Pb12 2–), which are highly stable and symmetric cage clusters. The names for these two clusters derive from their icosahedral (Ih) symmetry and delocalized spherical π-bonding that are characteristics of buckminsterfullerene C60. Stannaspherene and plumbaspherene have diameters comparable to that of C60 and can be considered as inorganic analogs of the buckyball. The large internal space in Sn12 2– has been shown to be able to trap any transition metal atom to form new endohedral cage clusters, M@Sn12 –, analogous to endohedral fullerenes. The doped atom in M@Sn12 – keeps its quasi-atomic nature with large magnetic moments. These endohedral cages form a rich class of new building blocks for cluster-assembled materials with tunable magnetic, electronic, and chemical properties. During our attempt to synthesize endohedral stannaspherenes, we crystallized a new Pd2@Sn18 4– cluster, which can be viewed as the fusion of two Pd@Sn12 2– clusters. This result suggests that stannaspherene, plumbaspherene, and a large number of their endohedrally doped species can be synthesized in the bulk.
2008. "Characterization and Acid-Mobilization Study of Iron-Containing Mineral Dust Source Materials." Journal of Geophysical Research. D. (Atmospheres) 113(D5):Art. No. D05202. doi:10.1029/2007JD009332 Abstract Processes that solubilize the iron in mineral dust aerosols may increase the amount of iron supplied to ocean surface waters, and thereby stimulate phytoplankton productivity. It was recently proposed that mixing of mineral dusts with SO2 and HNO3 produces extremely acidic environments that favor the formation of bioavailable Fe(II). Here, four authentic mineral dust source materials (Saudi Beach sand (SB), Inland Saudi sand (IS), Saharan Sand (SS) and China Loess (CL)) and one commercial reference material (Arizona Test Dust (AZTD)) were spectroscopically characterized, and their dissolution at pH 1 was examined in aqueous batch systems. Spectroscopic analyses indicated that the bulk and near-surface region of all samples possessed similar elemental compositions and that iron was unevenly distributed among dust 10 particles. Mössbauer spectroscopy revealed Fe(III) in all samples, although SB, CL and AZTD also contained appreciable Fe(II). Both Fe(II) and Fe(III) were primarily substituted into aluminosilicates, although CL, AZTD and IS also contained Fe(III) oxides. Total iron solubility (defined as the summed concentration of dissolved Fe(II) and Fe(III) measured after 24 h) ranged 14 between 4-12% of the source materials’ iron content, but did not scale with either the surface area or the iron content of the samples. This suggests that other factors such as iron speciation and mineralogy may play a key role in iron solubility. Also, the elevated nitrate concentrations encountered from nitric acid at pH 1 suppressed dissolution of Fe(II) from AZTD, CL and SB particles, which we propose results from the surface-mediated, non-photochemical reduction of nitrate by Fe(II).