Scientific Publications 2009
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2009. "Spectral Properties of Cs and Ba on Cu(111) at Very Low Coverage: Two-photon Photoemission Spectroscopy and Electronic Structure Theory." Physical Review. B, Condensed Matter and Materials Physics 80(24):245419. doi:10.1103/PhysRevB.80.245419 Abstract The adsorption of Cs and Ba on Cu(111) is investigated by means of one- and two-photon photoemission experiments and theoretically by first-principles calculations. The spectral properties of these systems, induced by both surface and adatom states, are studied at submonolayer coverage through angle-resolved measurements. A coverage-dependent analysis is also exploited in the assignment of the observed electronic states. The comparison with ab initio calculations allows identification of all the spectral features induced by Cs and Ba chemisorption. The theoretical analysis concerns the limiting single adatom case, treated in an embedding approach with a one-dimensional potential for the surface. The agreement between the calculated density of states and the experimental spectra confirms that the model substrate retains all the relevant physics entering in the adsorption process. The differences between the electronic structures of Cs and Ba on the Cu(111) surface can be attributed to the group-dependent screening of the core potentials as manifested by the ionic radii and ionization potentials (alkali vs alkaline earth).
2009. "Mexico City Aerosol Analysis during MILAGRO using High Resolution Aerosol Mass Spectrometry at the Urban Supersite (T0). Part 1: Fine Particle Composition and Organic Source Apportionment." Atmospheric Chemistry and Physics 9(17):6633-6653. Abstract Submicron aerosol was analyzed during the MILAGRO field campaign in March 2006 at the T0 urban supersite in Mexico City with a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and complementary instrumentation. Mass concentrations, diurnal cycles, and size distributions of inorganic and organic species are similar to results from the CENICA supersite in April 2003 with organic aerosol (OA) comprising about half of the fine PM mass. Positive Matrix Factorization (PMF) analysis of the high resolution OA spectra identifies three major components: chemically-reduced urban primary emissions (hydrocarbon-like OA, HOA), oxygenated OA (OOA, mostly secondary OA or SOA), and biomass burning OA (BBOA) that correlates with levoglucosan and acetonitrile. BBOA includes several very large plumes from regional fires and likely also some refuse burning.
2009. "Electron-Stimulated Reactions and O-2 Production in Methanol-Covered Amorphous Solid Water Films." Journal of Chemical Physics 130(10):Art. No. 104710. Abstract The low-energy, electron-stimulated desorption (ESD) of molecular products from amorphous solid water (ASW) films capped with methanol is investigated versus methanol coverage (0 - 4 x 1015 cm-2) at 50 K using 100 eV incident electrons. The major ESD products from a monolayer of methanol on ASW are quite similar to the ESD products from bulk methanol film: H2, CH4, H2O, C2H6, CO, CH2O, and CH3OH. For 40 ML ASW films, the molecular oxygen, hydrogen, and water ESD yields from the ASW are suppressed with increasing methanol coverage, while the CH3OH ESD yield increases proportionally to the methanol coverage. The suppression of the water ESD products by methanol is consistent with the non-thermal reactions occurring preferentially at or near the ASW/vacuum interface and not in the interior of the film. The water and molecular hydrogen ESD yields from the water layer decrease exponentially with the methanol cap coverage with 1/e constants of ~ 0.6 x 1015 cm-2 and 1.6 x 1015 cm-2, respectively. In contrast, the O2 ESD from the water layer is very efficiently quenched by small amounts of methanol (1/e ~ 6.5 x 1013 cm-2). The rapid suppression of O2 production by small amounts of methanol is due to reactions between CH3OH and the precursors for the O2 - mainly OH radicals. A kinetic model for the O2 ESD which semi-quantitatively accounts for the observations is presented.
2009. "Deletion of GPR40 Impairs Glucose-Induced Insulin Secretion In Vivo in Mice Without Affecting Intracellular Fuel Metabolism in Islets ." Diabetes 58(11):2607-2615. Abstract The G protein-coupled receptor GPR40 mediates fatty-acid potentiation of glucose-stimulated insulin secretion, but its contribution to insulin secretion in vivo and mechanisms of action remain uncertain. This study was aimed to ascertain whether GPR40 controls insulin secretion in vivo and modulates intracellular fuel metabolism in islets. We observed that glucose- and arginine-stimulated insulin secretion, assessed by hyperglycemic clamps, was decreased by approximately 60% in GPR40 knock-out (KO) fasted and fed mice, without changes in insulin sensitivity assessed by hyperinsulinemic-euglycemic clamps. Glucose and palmitate metabolism were not affected by GPR40 deletion. Lipid profiling revealed a similar increase in triglyceride and decrease in lysophosphatidylethanolamine species in WT and KO islets in response to palmitate. These results demonstrate that GPR40 regulates insulin secretion in vivo not only in response to fatty acids but also to glucose and arginine, without altering intracellular fuel metabolism.
2009. "Chemisorption of Transition-Metal Atoms on Boron- and Nitrogen-Doped Carbon Nanotubes: Energetics and Geometric and Electronic Structures." Journal of Physical Chemistry C 113(17):7069 - 7078. doi:10.1021/jp9000913 Abstract The well-defined binding between transition-metals (TM) and the sidewall of carbon nanotubes (CNTs) plays a key role in the performance of CNT-based anoelectronics, as well as the stability of catalysts used in either heterogeneous catalysis or fuel-cell electrocatalysis. Spin-polarized density functional theory calculations demonstrate that either boron or nitrogen doping can increase the binding strength of TM atoms with singlewall carbon nanotubes (SWCNTs), and comparatively, boron doping is more effective. The binding nature can be identified as chemisorption, based on the magnitude of the binding energy and the formation of multiple bonds. The chemisorbed TM atoms can modify the electronic structure of the doped nanotubes in various ways, depending upon the TM and helicity of the CNT, rendering the TM/doped-SWCNT composite viable for a wide range of applications. A total of 11 technologically relevant TMs adsorbed on two distinct and stable doped-SWCNT models have been investigated in this study. The doping sites are arranged in either a locally concentrated or uniform fashion within semiconducting SWCNT(8,0) and metallic SWCNT(6,6). The results serve as a starting point for studying larger, more complex TM nanostructures anchored on the sidewall of boron- or nitrogen-doped CNTs.
2009. "Electronic Structure Calculations of Gas Adsorption on Boron-doped CarbonNanotubes Sensitized with Tungsten." Chemical Physics Letters 482(4-6):274-280. doi:10.1016/j.cplett.2009.10.008 Abstract Density-functional theory methods are used to investigate the adsorption of nine prevalent gas molecules (H2, O2, CO, CO2, NO, NO2, H2O, CH3OH, and NH3) on a carbon nanotube-based support material. The support is a boron-doped, single-walled carbon nanotube, which has been sensitized by the adsorption of tungsten metal clusters. Our calculations demonstrate that this hybrid adsorbent material is able to adsorb the gas molecules with varied affinity, and these interactions are characterized by analyzing the features in the projected density-of-states for each system. These calculations represent a critical step in designing high-fidelity sensor materials, selective adsorbents, and more effective catalysts.
2009. "First-principles Study of Methane Dehydrogenation on a Bimetallic Cu/Ni(111) Surface." Journal of Chemical Physics 131(17):174702/1-174702/11. doi:10.1063/1.3254383 Abstract We present density-functional theory calculations of the dehydrogenation of methane and CHx (x =1–3) on a Cu/Ni(111) surface, where Cu atoms are substituted on the Ni surface at a coverage of 1/4 monolayer. As compared to the results on other metal surfaces, including Ni(111), a similar activation mechanism with different energetics is found for the successive dehydrogenation of CH4 on the Cu/Ni(111) surface. In particular, the activation energy barrier (Eact) for CH→C+H is found to be 1.8 times larger than that on Ni(111), while Eact for CH4→CH3+H is 1.3 times larger. Considering the proven beneficial effect of Cu observed in the experimental systems, our findings reveal that the relative Eact in the successive dehydrogenation of CH4 plays a key role in impeding carbon formation during the industrial steam reforming of methane. Our calculations also indicate that previous scaling relationships of the adsorption energy (Eads) for CHx (x=1–3) and carbon on pure metals also hold for several Ni(111)-based alloy systems.
2009. "Transition-Metal Strings Templated on Boron-Doped Carbon Nanotubes: A DFTInvestigation." Journal of Physical Chemistry C 113(34):15346-15354. doi:10.1021/jp9052715 Abstract The binding nature, magnetic, and electronic properties of transition-metal (TM) monatomic chains anchored on boron-doped single-walled carbon nanotubes (B-SWCNTs) are studied using density-functional theory. The TM systems studied here include Au, Pt, Ru, Pd, Ag, Co, Ni, Cu, W, and Ti, which are well-known for their technical importance. In conjunction, prototype semiconducting SWCNT(8,0) and metallic SWCNT(6,6) were chosen to model the general features of B-doped SWCNTs. It is found that the TM-strings exhibit well-defined covalent bonds with the boron-doped SWCNTs, in contrast to the pristine SWCNTs. The TMstring/ B-SWCNT composites exhibit high stability and unexpected electronic properties, which are relevant to applications in nanoelectronics, spintronics, nanocatalysis, and sensor devices.
2009. "Performance of DFT Methods in the Calculation of Optical Spectra of TCF-Chromophores." Journal of Chemical Theory and Computation 5(10):2835-2846. doi:10.1021/ct900231r Abstract We present electronic structure calculations of the ultraviolet/visible (UV-Vis) spectra of highly active push-pull chromophores containing tricyanofuran (TCF) acceptor group. In particular, we have applied the recently developed long-range corrected Baer-Neuhauser-Livshits (BNL) exchange-correlation functional. The performance of this functional compares favorably with other density functional theory (DFT) approaches, including the CAM-B3LYP functional. The accuracy of UV-Vis results for these molecules is best at low values of attenuation parameters (γ) for both BNL and CAM-B3LYP functionals. The optimal value of γ is different for the charge-transfer (CT) and π-π* excitations. The BNL and PBE0 exchange correlation functionals capture the CT states particularly well while the π-π* excitations are less accurate and system dependent. Chromophore conformations, which considerably affect the molecular hyperpolarizability, do not significantly influence the UV-Vis spectra on average. As expected, the color of chromophores is a sensitive function of modifications to its conjugated framework, and is not significantly affected by increasing aliphatic chain length linking a chromophore to a polymer. For selected push-pull aryl-chromophores, we find a significant dependence of absorption spectra on the strength of diphenylaminophenyl donors.
2009. "Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation." PLoS One 4(3):e4809. doi:10.1371/journal.pone.0004809 Abstract In recent years the profound importance of sRNA-mediated translational/post-transcriptional regulation has been increasingly appreciated. However, the global role played by translational regulation in control of gene expression has never been elucidated in any organism for the simple reason that global proteomics methods required to accurately characterize post-transcriptional processes and the knowledge of translational control mechanisms have only become available within the last few years. The proteins Hfq and SmpB are essential for the biological activity of a range of regulatory sRNAs and thus provide a means to identify potential targets of sRNA regulation. We performed a sample-matched global proteomics and transcriptional analysis to examine the role of Hfq and SmpB in global protein translation and virulence using the Salmonella typhimurium model system. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all Salmonella proteins, respectively, with limited correlation between transcription and protein expression. This is the first report suggesting that SmpB could be a general translational regulator. The broad spectrum of proteins modulated by Hfq was also surprising including central metabolism, LPS biosynthesis, two-component regulatory systems, quorum sensing, SP1-TTSS, oxidative stress, fatty acid metabolism, nucleoside and nucleotide metabolism, envelope stress, aminoacyl-tRNA synthetases, amino acid biosynthesis, peptide transport, and motility.. The extent of global regulation of translation by Hfq is unexpected, with profound effects in all stages of Salmonella’s life cycle. Our results represent the first global systems-level analysis of translational regulation; the elucidated potential targets of sRNA regulation from our analysis will facilitate the characterization of sRNA control mechanisms and their targets mRNAs by the broader scientific community by providing global-scale insights.
2009. "Cerium Oxyhydroxide Clusters: Formation, Structure and Reactivity." Journal of Physical Chemistry A 113(22):6239-6252. doi:10.1021/jp9015432 Abstract Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [CexOy] ions and neutrals. These initially-formed species react with water, principally forming closed-shell (c-s) oxohydroxy species that are described by the general formula [CexOy(OH)z]-. In general, the extent of hydroxylation varies from a value of 3 OH per Ce atom when x = 1 to a value slightly greater than 1 for x > 8. The Ce3 and Ce6 species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and x = 4. Conversely, the x = 6 cluster is significantly less hydroxylated. Density functional theory (DFT) modeling of the cluster structures show that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce3 oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce6 oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the c-s clusters, open-shell (o-s) oxyhydroxides and superoxides are also formed, and they become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to stabilize a non-bonding electron. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases, however this trend is interrupted at Ce13, which is significantly more stable compared to neighboring congeners, suggesting formation of a dehydrated Keggin-type structure.
2009. "Experimental and Theoretical Investigations of CB8-:Towards Rational Design of Hypercoordinated Planar Chemical Species." Physical Chemistry Chemical Physics. PCCP 11(42):9840-9849. doi:10.1039/b908973j Abstract We demonstrated in our joint photoelectron spectroscopic and ab initio study that wheel-type structures with a boron ring are not appropriate for designing planar molecules with a hypercoordinate central carbon on the example of CB8, and CB8 clusters. According to our chemical bonding model, in the wheel type structures the central atom is involved in delocalized bonding, while peripheral atoms are involved in both delocalized bonding and 2c-2e -bonding. Since carbon is more electronegative than boron it favors peripheral positions where it can participate in 2c-2e -bonding. To design a chemical species with a central hypercoordinate carbon atom, one should consider electropositive ligands, which would have lone pairs instead of 2c-2e peripheral bonds. We presented a chemical bonding model capable of rationalizing and predicting structures either with a boron ring or a central planar carbon. This represents the first step toward rational design of nano- and subnano-structures with tailored properties.
