Scientific Publications 2006
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K
2006. "Higher-Order Equation-of-Motion Coupled-Cluster Methods for Ionization Processes." Journal of Chemical Physics 125:074111. Abstract Abstract for this article not available at this time.
2006. "Higher-Order Equation-of-Motion Coupled-Cluster Methods for Ionization Processes." Journal of Chemical Physics 125:074111. doi:10.1063/1.2244570 Abstract No abstract available for this journal article at this time.
2006. "Prediction of Experimental Methanol Decomposition Rates on Platinum from First Principles." Topics in Catalysis 37(1):17-28. doi:10.1007/s11244-006-0001-1 Abstract A portion of this work was conducted at EMSL, a national scientific user facility. A microkinetic model for methanol decomposition on platinum is presented. The model incorporates competitive decomposition pathways, beginning with both O–H and C–H bond scission in methanol, and uses results from density functional theory (DFT) calculations [Greeley and Mavrikakis, J. Am. Chem. Soc. 124 (2002) 7193, Greeley and Mavrikakis, J. Am. Chem. Soc. 126 (2004) 3910]. Results from reaction kinetics experiments show that the rate of H2 production increases with increasing temperature and methanol concentration in the feed and is only nominally affected by the presence of CO or H2 with methanol. The model, based on the values of binding energies, pre-exponential factors and activation energy barriers derived from first principles calculations, accurately predicts experimental reaction rates and orders. The model also gives insight into the most favorable reaction pathway, the rate-limiting step, the apparent activation energy, coverages, and the effects of pressure. It is found that the pathway beginning with the C–H bond scission (CH3OH→H2COH→HCOH→CO) is dominant compared with the path beginning with O–H bond scission. The cleavage of the first C–H bond in methanol is the rate-controlling step. The surface is highly poisoned by CO, whereas COH appears to be a spectator species.
2006. "B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations." Biophysical Journal 91(8):2956-2965. doi:10.1529/biophysj.106.087163 Abstract The twist flexibility of DNA is central to its many biological functions. Explicit solvent molecular dynamics simulations in combination with an umbrella sampling restraining potential have been employed to study induced twist deformations in DNA. Simulations allowed us to extract free energy profiles for twist deformations and were performed on six DNA dodecamer duplexes to cover all 10 possible DNA basepair steps. The shape of the free energy curves was similar for all duplexes. The calculated twist deformability was in good agreement with experiment and showed only modest variation for the complete duplexes. However, the response of the various basepair steps on twist stress was highly nonuniform. In particular, pyrimidine/ purine steps were much more flexible than purine/purine steps followed by purine/pyrimidine steps. It was also possible to extract correlations of twist changes and other helical as well as global parameters of the DNA molecules. Twist deformations were found to significantly alter the local as well as global shape of the DNA modulating the accessibility for proteins and other ligands. Severe untwisting ofDNAbelow an average of 2° per basepair step resulted in the onset of a global structural transition with a significantly smaller twist at one end of the DNA compared to the other.
2006. "Ferromagnetism and structure of epitaxial Cr-doped anatase TiO2 thin films." Physical Review. B, Condensed Matter and Materials Physics 73(15):155327 (12 p.). doi:10.1103/PhysRevB.73.155327 Abstract The materials and magnetic properties of Cr-doped anatase TiO2 thin films deposited on LaAlO3(001) and SrTiO3(001) substrates by oxygen-plasma-assisted molecular beam epitaxy have been studied in detail to elucidate the origin of ferromagnetic ordering. Cr substitution for Ti in the anatase lattice, with no evidence of Cr interstitials, segregation, or secondary phases, was independently confirmed by transmission electron microscopy (TEM) with energy dispersive x-ray (EDX) spectroscopy, extended x-ray absorption fine structure (EXAFS), and Rutherford backscattering spectrometry (RBS) in the channeling geometry. Epitaxial films deposited at ~0.1 Å/s were found to have a highly defected crystalline structure, as quantified by high resolution x-ray diffraction (XRD). These films were also ferromagnetic at room temperature with a moment of ~0.5 B/Cr, Curie temperatures in the range of 400 – 700°C, and exhibited shape and in-plane magnetocrystalline anisotropy. However, no free carrier spin polarization was observed by Hall effect measurements, raising questions about the mechanism of magnetism. Films deposited slowly (~0.015 Å/s) possessed a nearly perfect crystalline structure as characterized by XRD. Contrary to expectations, these films exhibited negligible ferromagnetism at all Cr concentrations. Annealing in vacuum to generate additional oxygen defects and free carrier electrons did not significantly increase the ferromagnetic ordering in either fast- or slow-grown films. These results contradict both oxygen-vacancy-derived free-carrier-mediated exchange and F-center-mediated bound magnetic polaron exchange mechanisms, and instead indicate the primary role of extended structural defects in mediating the ferromagnetic ordering in doped anatase films.
2006. "Magnetic properties of epitaxial Co-doped anatase TiO2 thin films with excellent structural quality." Journal of Vacuum Science and Technology B--Microelectronics and Nanometer Structures 24(4):2012-2017. doi:10.1116/1.2216723 Abstract The heteroepitaxy of Co-doped anatase TiO2 on LaAlO3(001) has been refined with the goal of determining the relationship between structural quality and magnetic ordering. By significantly reducing the deposition rate and substrate temperature, well-ordered Co:TiO2 films with unprecedented crystalline quality were obtained by oxygen-plasma-assisted molecular beam epitaxy, as characterized by x-ray diffraction. These films exhibit uniform Co doping, with no evidence of Co segregation or secondary phases throughout the film depth or on the surface. Despite the improvement in crystalline quality and Co distribution, the films exhibit negligible ferromagnetism, with saturation moments of only ~0.1 B/Co. This loss of ferromagnetism is in stark contrast to faster-grown Co:TiO2 films, where a higher growth rate and substrate temperature typically result in lower crystalline quality, a highly non-uniform Co distribution, and average saturation moments of ~1.2 B/Co. The presence of ferromagnetism in faster-grown Co:TiO2 does not appear to arise from intrinsic point defects present in the bulk material, such as charge-compensating oxygen vacancies, but is instead attributed to the presence of extended structural defects.
2006. "Oxidation studies of CrAlON nanolayered coatings on steel plates." Surface & Coatings Technology 201(3-4):1685-1694. doi:10.1016/j.surfcoat.2006.02.053 Abstract The requirements of low cost and high-temperature corrosion resistance for bipolar interconnect plates in solid oxide fuel cell stacks have directed attention to the use of metal plates with oxidation resistant coatings. We have investigated the performance of steel plates with nanolayered coatings consisting of [CrON/AlON]n. The coatings were deposited using large-area filtered arc deposition technology, with various O/N pressure ratios, and subsequently annealed in air for up to 25 h at 800 °C. The composition, structure and surface morphology of the coated plates were characterized using RBS, nuclear reaction analysis, and AFM techniques. By altering the architecture and composition of the coatings, the rate of oxidation was reduced relative to the uncoated steel plates, and Fe diffusion from the substrate to the surface through the coating was significantly reduced.
2006. "Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry." Analytical Chemistry 78(22):7796-7801. Abstract We have developed a new procedure for fabricating fused silica emitters for electrospray ionization-mass spectrometry (ESI-MS) in which the end of a bare fused silica capillary is immersed into aqueous hydrofluoric acid, and water is pumped through the capillary to prevent etching of the interior. Surface tension causes the etchant to climb the capillary exterior, and the etch rate in the resulting meniscus decreases as a function of distance from the bulk solution. Etching continues until the silica touching the hydrofluoric acid reservoir is completely removed, essentially stopping the etch process. The resulting emitters have no internal taper, making them much less prone to clogging compared to e.g. pulled emitters. The high aspect ratios and extremely thin walls at the orifice facilitate very low flow rate operation; stable ESI-MS signals were obtained for model analytes from 5-μm-diameter emitters at a flow rate of 5 nL/min with a high degree of inter-emitter reproducibility. In extensive evaluation, the etched emitters were found to enable approximately four times as many LC-MS analyses of proteomic samples before failing compared with conventional pulled emitters. The fabrication procedure was also employed to taper the ends of polymer monolith-containing silica capillaries for use as ESI emitters. In contrast to previous work, the monolithic material protrudes beyond the fused silica capillaries, improving the monolith-assisted electrospray process.
2006. "Computer Simulation of Electron Transfer at Hematite Surfaces." Geochimica et Cosmochimica Acta 70(8):1888-1903. doi:10.1016/j.gca.2005.12.021 Abstract Molecular dynamics simulations in combination with ab initio calculations were carried out to determine the rate of electron transfer in bulk hematite (α-Fe2O3) and at two low-index surfaces, namely the (012) and (001) surfaces. The electron transfer reactions considered here involve the II/III valence interchange between nearest-neighbor iron atoms. Two electron transfer directions were investigated namely the basal plane and c direction charge transfers. Electron transfer rates obtained in bulk hematite were in good agreement with ab initio electronic structure calculations thus validating the potential model. The surfaces were considered both in vacuum and in contact with an equilibrated aqueous solution. The reorganization energy is found to increase significantly at the first surface layer and this value is little affected by the presence of water. In addition, in the case of the (012) surface, the electronic coupling matrix element for the topmost basal plane transfer was calculated at the Hartree-Fock level and was found to be weak compared to the corresponding charge transfer in the bulk. Therefore, most surfaces show a decrease in the rate of charge transfer at the surface. However, where iron atoms involved in the charge transfer reaction are directly coordinated to water molecules, water lowers the free energy of activation to a great extent and provides a large driving force for electrons to diffuse toward the bulk thus opposing the intrinsic surface effect. The surfaces considered in this work show different charge transfer properties. Hematite has been shown to exhibit anisotropic conductivity and thus different surfaces will show different intra- and inter-layer rates depending on their orientation. Moreover, the calculations of charge transfers at the hydroxyl- and iron-terminated (001) surfaces revealed that surface termination has a significant effect on the charge transfer parameters in the vicinity of the surface. Finally, our findings indicate that undercoordinated terminal iron atoms could act as electron traps at the surface.
2006. "High Resolution studies of Tropolone in the So and S1 Electronic States: Isotope Driven Dynamics in the Zero-Point Energy Levels." Journal of Chemical Physics 124(7):074309. doi:10.1063/1.2165652 Abstract Rotationally resolved microwave (MW) and ultraviolet (UV) spectra of jet-cooled tropolone have been obtained in S0 and S1 electronic states using Fourier-transform microwave and UV laser/molecular beam spectrometers. In the ground electronic state, the MW spectra of all heavy atom isotopomers including one 18O and four 13C isotopomers were observed in natural abundance. The OD isotopomer was obtained from isotopically enriched samples. The two lowest tunneling states of each isotopomer except 18O have been assigned. For the asymmetric 13C structures, the magnitudes of tunneling-rotation interactions diminished with decreasing distance between the heavy atom and the tunneling proton. In the limit of closest approach, the v=0 state of 18O was well-fit to asymmetric rotor Hamiltonians, signifying a drastic change in the tautomerization dynamics. Comparisons of the substituted atom coordinates with theoretical predictions at the MP2/aug-cc-pVTZ level of theory suggest the localized v=0 and v=1 wavefunctions of the heavier isotopes favor the C-OH and C=O forms of tropolone, respectively. The only exception occurs for 13C-OH and 13C=O structures which correlate to the v=1 and v=0 states, respectively. These preferences reflect kinetic isotope effects as quantitatively verified by the calculated zero point energy differences (ΔZPE's) between members of the asymmetric atom pairs. The ΔZPE's are principally defined by contributions from the out-of-plane zero-point motions and aid in elucidating the mode-specific nature of the tunneling splittings. From rotationally resolved data of the 0+-0+/0+-0- and 0--0-/0--0+ bands in S1, lineshape fits have yielded different Lorentzian linewidths, increasing from 131.1(8) MHz to 143.3(8) MHz, respectively. This 12.2(8) MHz increase over the 18.04(2) cm-1 tunneling splitting interval in S1 correlates with a nearly monotonic increase in the intersystem crossing rate when extrapolated to higher vibrational excess energies in S1, suggesting a dependence of the non-radiative decay dynamics on tunneling state.
2006. "Redox-linked conformation change and electron transfer between monoheme c-type cytochromes and oxides." Geochimica et Cosmochimica Acta 70(17):4332-4342. doi:10.1016/j.gca.2006.06.1561 Abstract Electron transfer between redox active proteins and mineral oxides is important in a variety of natural as well as technological processes, including electron transfer from dissimilatory metal-reducing bacteria to minerals. One of the pathways that could trigger electron transfer between proteins and minerals is redox-linked conformation change. We present electrochemical evidence that mitochondrial cytochrome c (Mcc) undergoes significant conformation change upon interaction with hematite and indium-tin oxide (ITO) surfaces. The apparent adsorption-induced conformation change causes the protein to become more reducing, which makes it able to transfer electrons to the hematite conduction band. Although Mcc is not a protein thought to be involved in interaction with mineral surfaces, it shares (or can be conformed so as to share) some characteristics with multiheme outer-membrane cytochromes thought to be involved in the transfer of electrons from dissimilatory iron-reducing bacteria to ferric minerals during respiration. We present evidence that a 10.1 kDa monohoeme cytochrome isolated and purified from Acidiphilium cryptum, with properties similar to those of Mcc, also undergoes conformation change as a result of interaction with hematite surfaces.
2006. "Structural and redox properties of mitochondrial cytochrome c co-sorbed with phosphate on hematite (α-Fe2O3) surfaces." Journal of Colloid and Interface Science 303(2):404-414. doi:10.1016/j.jcis.2006.07.070 Abstract The interaction of metalloproteins with oxides has implications not only for bioanalytical systems and biosensors but also in the areas of biomimetic photovoltaic devices, bioremediation, and bacterial metal reduction. Here, we investigate mitochondrial ferricytochrome c (Cyt c) co-sorption with 0.01 and 0.1 M phosphate on hematite (α-Fe2O3) surfaces as a function of pH (2–11). Although Cyt c sorption to hematite in the presence of phosphate is consistent with electrostatic attraction, other forces act upon Cyt c as well. The occurrence of multilayer adsorption, and our AFM observations, suggest that Cyt c aggregates as the pH approaches the Cyt c isoelectric point. In solution, methionine coordination of heme Fe occurs only between pH 3 and 7, but in the presence of phosphate this coordination is retained up to pH 10. Electrochemical evidence for the presence of native Cyt c occurs down to pH 3 and up to pH 10 in the absence of phosphate, and this range is extended to pH 2 and 11 in the presence of phosphate. Cyt c that initially adsorbs to a hematite surface may undergo conformation change and coat the surface with unfolded protein such that subsequently adsorbing protein is more likely to retain the native conformational state. AFM provides evidence for rapid sorption kinetics for Cyt c co-sorbed with 0.01 or 0.1 M phosphate. Cyt c co-sorbed with 0.01 M phosphate appears to unfold on the surface of hematite while Cyt c co-sorbed with 0.1 M phosphate possibly retains native conformation due to aggregation.
2006. "Effect of Barium Loading on the Desulfation of Pt-BaO/Al2O3 Studied by H2 TPRX, TEM, Sulfur K-edge XANES, and in Situ TR-XRD." Journal of Physical Chemistry B 110(21):10441-10448. doi:10.1021/jp060119f Abstract Desulfation processes were investigated over sulfated Pt BaO/Al2O3 with different barium loading (8 wt% and 20 wt%) by using H2 temperature programmed reaction (TPRX), transmission electron microscope (TEM) with energy dispersive spectroscopy (EDS), sulfur K-edge X-ray absorption near-edge spectroscopy (XANES), and in situ time-resolved X-ray diffraction (TR-XRD) techniques. Both sulfated samples (8 wt% and 20 wt%) form sulfate species (primarily BaSO4) as evidenced by S K-edge XANES and in situ TR-XRD. However, the desulfation behavior is strongly dependant on the barium loading. Sulfated Pt BaO(8)/Al2O3, consisting predominantly of surface BaO/BaCO3 species, displays more facile desulfation by H2 at lower temperatures than sulfated Pt BaO(20)/Al2O3, a material containing primarily bulk BaO/BaCO3 species. Therefore, after desulfation with H2 up to 1073 K, the amount of the remaining sulfur species on the former, mostly as BaS, is much less than on the latter. This suggests that the initial morphology differences between the two samples play a crucial role in determining the extent of desulfation and the temperature at which it occurs. It is concluded that the removal of sulfur is significantly easier at lower barium loading. This finding can potentially be important in developing more sulfur resistant LNT catalyst systems.
2006. "Challenges in Biocatalysis for Enzyme-Based Biofuel Cells." Biotechnology Advances 24:296-308. Abstract Enzyme-based biofuel cells are attracting attention rapidly partially due to the promising advances reported recently. However, there are issues to be addressed before biofuel cells become competitive in practical applications. Two critical issues are short lifetime and poor power density, both of which are related to enzyme stability, electron transfer rate, and enzyme loading. Recent progress in nanobiocatalysis opens the possibility to improve in these aspects. Many nano-structured materials, such as mesoporous media, nanoparticles, nanofibers, and nanotubes, have been demonstrated as efficient hosts of enzyme immobilization. It is evident that, when nanostructure of conductive materials are used, the large surface area of these nanomaterials can increase the enzyme loading and facilitate reaction kinetics, and thus improving the power density of biofuel cells. In addition, research efforts have also been made to improve the activity and stability of immobilized enzymes by using nanostructures. It appears to be reasonable to us to expect that progress in nanostuctured biocatalysts will play a critical role in overcoming the major obstacles in the development of powerful biofuel cells.
2006. "Magnetic Fluorescent Delivery Vehicle using Uniform Mesoporous Silica Spheres Embedded with Monodisperse Magnetic and Semiconductor Nanocrystals." Journal of the American Chemical Society 128(3):688-689. Abstract Uniform sized colloidal nanocrystals have attracted much attention, because of their unique magnetic and optical properties, as compared with those of their bulk counterparts. Especially magnetic nanocrystals and quantum dots have been intensively pursued for biomedical applications such as contrast enhancement agents in magnetic resonance imaging, magnetic carriers for drug delivery system, biological labeling and diagnostics. Due to their large pore sizes and high surface areas, mesoporous materials and its composites with nanocrystals have attracted considerable attention. In order to use the nanocrystals as functional delivery carriers and catalytic supports, nanocrystals coated with porous silica shells are desirable. Herein, we report a synthetic procedure for the fabrication of monodisperse nanocrystals embedded in uniform pore-sized mesoporous silica spheres. As a representative example, we synthesized monodisperse magnetite (Fe3O4) nanocrystals embedded in mesoporous silica spheres and both magnetite nanocrystals and CdSe/ZnS quantum dots embedded in mesoporous silica spheres. Furthermore, these mesoporous silica spheres were applied to the uptake and controlled release of drugs.
2006. "Nanostructures for enzyme stabilization." Chemical Engineering Science 61(3):1017-1026. Abstract The last decade has witnessed notable breakthroughs in nanotechnology with development of various nanostructured materials such as mesoporous materials and nanoparticles. These nanostructures have been used as a host for enzyme immobilization via various approaches, such as enzyme adsorption, covalent attachment, enzyme encapsulation, and sophisticated combinations of methods. This review discusses the stabilization mechanisms behind these diverse approaches; such as confinement, pore size and volume, charge interaction, hydrophobic interaction, and multipoint attachment. In addition, we will introduce recent rigorous approaches to improve the enzyme stability in these nanostructures or develop new nanostructures for the enzyme stabilization. Especially, we will introduce our recent invention of a nanostructure, called single enzyme nanoparticles (SENs). In the form of SENs, each enzyme molecule is surrounded with a nanometer scale network, resulting in stabilization of enzyme activity without any serious limitation for the substrate transfer from solution to the active site. SENs can be further immobilized into mesoporous silica with a large surface area, providing a hierarchical approach for stable, immobilized enzyme systems for various applications, such as bioconversion, bioremediation, and biosensors.
2006. "Layer-by-Layer Growth of Thin Amorphous Solid Water Films on Pt(111) and Pd(111)." Journal of Chemical Physics 125(4):044713-1 - 044713-12. doi:10.1063/1.2218844 Abstract The growth of amorphous solid water (ASW) films on Pt(111) is investigated using rare gas (e.g. Kr) physisorption. Temperature programmed desorption of Kr is sensitive to the structure of thin water films and can be used to assess the growth modes of these films. At all temperatures that are experimentally accessible (20 – 155 K), the first layer of water wets Pt(111). Over a wide temperature range (20 – 120 K), ASW films wet the substrate and grow approximately layer-by-layer for at least the first 3 layers. In contrast to the ASW films, crystalline ice films do not wet the water monolayer on Pt(111). Virtually identical results were obtained on epitaxial Pd(111) films grown on Pt(111). The desorption rates of thin ASW and crystalline ice films suggest that the relative free energies of the films are responsible for the different growth modes. However at low temperatures, surface relaxation or “transient mobility” is primarily responsible for the relative smoothness of the films.
2006. "Coherent Raman Spectra of the nu(1) Mode of 10BF3 and 11BF3." Journal of Molecular Spectroscopy 237(1):97-103. Abstract High resolution (0.001cm-1) coherent anti-Stokes Raman spectroscopy (CARS) was used to directly examine the v1 symmetric stretching mode of the planar symmetric D3h molecules 10BF3 and 11BF3. Simulations of the spectra were done using v1 rovibrational parameters deduced from published infrared hot-band and difference-band studies and the close similarity to the observed CARS spectra confirms the validity of the infrared constants. No significant perturbations by Fermi resonance or Coriolis interactions with nearby states are observed, in marked contrast to the case of sulfur trioxide, a similar D3h molecule recently studied. In the harmonic approximation, the 10BF3 and 11BF3 v1 Q- branches would be identical since the isotopic substitution is at the center of mass but, interestingly, the v1 stretching frequency for 11BF3 is found to be 0.198 cm-1 higher than for the lighter 10BF3 isotopomer. This counterintuitive result is reproduced almost exactly (0.200 cm -1) by ab initio calculations (B3LYP/cc-pVTZ) that included evaluation of cubic and quartic forced constants and xij anharmonicity constants. The ab initio computations also predict to within 1% the ∆B, ∆C changes in the rotational constants in going from the ground state to the v1=1 vibrational level. The results illustrate nicely the complementary interplay of modern infrared, Raman, and ab initio methods in obtaining and analyzing rovibrational spectra.
2006. "Direct kinetic correlation of carriers and ferromagnetism in Co2+ : ZnO." Physical Review Letters 97:037203-1 - 037203-4. doi:10.1103/PhysRevLett.97.037203 Abstract We report the use of controlled introduction and removal of Zni to test the hypothesis that high-Curie-temperature ferromagnetism in cobalt-doped ZnO (Co2+:ZnO) is mediated by carriers. Using oriented epitaxial Co2+:ZnO films grown by chemical vapor deposition, kinetics measurements were used to correlate the oxidative quenching of ferromagnetism with the diffusion and oxidation of interstitial zinc. These results demonstrate controlled systematic variation of a key parameter involved in the ferromagnetism of Co2+:ZnO, namely interstitial zinc, and in the process unambiguously reveal this ferromagnetism to be dependent upon carriers. The distinction between defect-bound and free carriers in Co2+:ZnO is discussed
2006. "Atomic structure of nitrate-binding protein crucial for photosynthetic productivity." Proceedings of the National Academy of Sciences of the United States of America 103(26):9820-9825. doi:10.1073/pnas.060251703 Abstract Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of all aquatic food chains by fixing carbon and nitrogen into cellular biomass. The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments particularly the open ocean (1, 2). It is therefore not surprising that NrtA, the solute-binding component of the high-affinity nitrate ABC transporter, is the single-most abundant protein in the plasma membrane of these bacteria (3). Here we describe the first structure of a nitratespecific receptor, NrtA from Synechocystis sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5Å. NrtA is significantly larger than other oxyanionbinding proteins, representing a new class of transport proteins. From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonatebinding protein. Therefore, these organisms created a novel solute-binding protein for two of the most important nutrients; inorganic nitrogen and carbon. The electrostatic charge distribution of NrtA appears to force the protein off of the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore. The structure not only details the determinants for nitrate selectivity in NrtA, but also the bicarbonate specificity in CmpA. Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively. Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate. This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.3 The nitrate ABC transporter of cyanobacteria is composed of four polypeptides (Figure 1): a high-affinity periplasmic solute-binding lipoprotein (NrtA), an integral membrane permease (NrtB), a cytoplasmic ATPase (NrtD), and a unique ATPase/solute-binding fusion protein (NrtC) that regulates transport (4). NrtA binds both nitrate and nitrite (Kd = 0.3 mM) and is necessary for cell survival when nitrate is the primary nitrogen source (5). The role of NrtA is to scavenge nitrate/nitrite from the periplasm for delivery to the membrane permease, NrtB. The passage of solute through the transmembrane pore is linked to ATP hydrolysis by NrtC and NrtD. NrtD consists of a single ATPase domain. In contrast, NrtC contains both an ATPase domain and a Cterminal solute-binding domain that shares 50% amino acid sequence similarity with NrtA, and is required for the ammonium-mediated inhibition of nitrate transport (6, 7). Aside from the homologous transporter for bicarbonate, CmpABCD, there are no other known examples of ABC transporters that have an ATPase/solute-binding fusion component. The specificity of the nitrate transporter is conferred by NrtA (4). NrtA is ~49% identical (60% similar) in amino acid sequence to the bicarbonate receptor CmpA. In its entirety, it does not have significant homology to any other known protein. To elucidate the molecular determinants of nitrate specificity, we determined the crystal structure of the Synechocystis 6803 NrtA to 1.5 Å. While the general shape of NrtA is akin to that of other solute binding proteins, NrtA clearly represents a new and unique structural variant of these ‘C clamp’ proteins. From this structure and sequence alignments of other bicarbonate and nitrate transporters, the molecular basis for solute selectivity is clear and suggests that regulatory domains of both icarbonate and nitrate transport systems bind nitrate. Based on these findings, a model is presented that 4 demonstrates how such synergistic regulation of bicarbonate and nitrate transport is important in conserving energy during the process of carbon fixation and nitrogen assimilation.
2006. "Static Dielectric Properties of Carbon Nanotubes from First Principles." Physical Review Letters 96:166801 1-4. doi:10.1103/PhysRevLett.96.166801 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. We characterize the response of isolated single-wall (SWNT) and multiwall (MWNT) carbon nanotubes and nanotube bundles to static electric fields using first-principles calculations and densityfunctional theory. The longitudinal polarizability of SWNTs scales as the inverse square of the band gap, while in MWNTs and bundles it is given by the sum of the polarizabilities of the constituent tubes. The transverse polarizability of SWNTs is insensitive to band gaps and chiralities and is proportional to the square of the effective radius; in MWNTs, the outer layers dominate the response. The transverse response is intermediate between metallic and insulating, and a simple electrostatic model based on a scale-invariance relation captures accurately the first-principles results. The dielectric response of nonchiral SWNTs in both directions remains linear up to very high values of applied field.
2006. "Effects of nanocrystalline CeO2 supports on the properties and performanceof Ni–Rh bimetallic catalyst for oxidative steam reforming of ethanol." Journal of Catalysis 238(2):430-440. doi:10.1016/j.jcat.2006.01.001 Abstract This study focuses on the effects of the CeO2 support properties on the catalyst properties and performance of bimetallic Ni–Rh/CeO2 catalysts containing 5 wt% Ni and 1 wt% Rh for the oxidative steam reforming (OSR) of ethanol for hydrogen production and fuel cell applications. Three CeO2 supports with different crystal sizes and surface areas were examined. The surface areas of these supports increases in the order of CeO2-I (74 m2/g) < CeO2-II (92 m2/g) < CeO2-III (154 m2/g), but their crystallite sizes were about 10.2, 29.3, and 6.5 nm, respectively. The properties of Ni–Rh/CeO2 catalysts were investigated by XRD, TPR, H2 chemisorption, and in situ XPS techniques. The Rh metal dispersion increased while the Ni metal dispersion decreased with decreasing crystallite sizes of CeO2. TPR studies revealed the existence of a Rh–CeO2 metal–support interaction as well as Ni–Rh interaction in the Ni–Rh bimetallic catalyst supported on CeO2-III with a crystallite size of about 6.5 nm. The in situ XPS studies corroborated the TPR results. The reduced Ni and Rh species were reversibly oxidized, suggesting the existence of Ni–Rh redox species rather than NiRh surface alloy in the present catalyst system. The Rh species became highly dispersed when the crystallite size of CeO2 support was smaller. Comparing the catalytic performance in the OSR of ethanol was compared with the properties of the catalysts demonstrated that both ethanol conversion and H2 selectivity increased and the selectivity for undesirable byproducts decreased with increasing Rh metal dispersion. Best catalytic performance for OSR was achieved by supporting Ni–Rh bimetallic catalysts on the nanocrystalline CeO2-III. The Ni–Rh/CeO2-III catalyst exhibited stable activity and selectivity during on-stream operations at 450 ◦C and as well as at 600 ◦C.
2006. "Reductive Biotransformation of Fe in Shale-Limestone Saprolite Containing Fe(III) Oxides and Fe(II)/Fe(III) Phyllosilicates." Geochimica et Cosmochimica Acta 70(14):3662–3676. doi:10.1016/j.gca.2006.05.004 Abstract A <2.0-mm fraction of a mineralogically complex subsurface sediment containing goethite and Fe(II)/Fe(III) phyllosilicates was incubated with Shewanella putrefaciens (strain CN32) and lactate at circumneutral pH under anoxic conditions to investigate electron acceptor preference and the nature of the resulting biogenic Fe(II) fraction. Anthraquinone-2,6-disulfonate (AQDS), an electron shuttle, was included in select treatments to enhance bioreduction and subsequent biomineralization. The sediment was highly aggregated and contained two distinct clast populations: i) a highly weathered one with “sponge-like” internal porosity, large mineral crystallites, and Fe-containing micas, and ii) a dense, compact one with fine-textured Fe-containing illite and nano-sized goethite, as revealed by various forms of electron microscopic analyses. Approximately 10 to 15% of the Fe(III)TOT was bioreduced by CN32 over 60 d in media without AQDS, whereas 24% and 35% of the Fe(III)TOT was bioreduced by CN32 after 40 and 95 d in media with AQDS. Little or no Fe2+, Mn, Si, Al, and Mg were evident in aqueous filtrates after reductive incubation. Mössbauer measurements on the bioreduced sediments indicated that both goethite and phyllosilicate Fe(III) were partly reduced without bacterial preference. Goethite was more extensively reduced in the presence of AQDS whereas phyllosilicate Fe(III) reduction was not influenced by AQDS. Biogenic Fe(II) resulting from phyllosilicate Fe(III) reduction remained in a layer-silicate environment that displayed enhanced solubility in weak acid. The mineralogic nature of the goethite biotransformation product was not determined. Chemical and cryogenic Mössbauer measurements, however, indicated that the transformation product was not siderite, green rust, magnetite, Fe(OH)2, or Fe(II) adsorbed on phyllosilicate or bacterial surfaces. Several lines of evidence suggested that biogenic Fe(II) existed as surface associated phase on the residual goethite, and/or as a Fe(II)-Al coprecipitate. Sediment aggregation and mineral physical and/or chemical factors were demonstrated to play a major role on the nature and location of the biotransformation reaction and its products.
2006. "Density Functional Theory in Transition-Metal Chemistry:A Self-Consistent Hubbard U Approach." Physical Review Letters 97(103001):1-4. doi:10.1103/PhysRevLett.97.103001 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. Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlatedelectron quantum chemistry calculations in test cases that range from the ground state of Fe₂ and Fe₂- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel selfconsistent procedure based on a linear-response approach.
2006. "Traps identification in Copper-Indium-Gallium-Sulfur-Selenide Solar Cells Completed with Various Buffer Layers by Deep Level Transient Spectroscopy ." Thin Solid Films 515(4):2625-2631. doi:10.1016/j.tsf.2006.03.046 Abstract Current-voltage characteristics of thin film semiconductor devices are greatly affected by surface and interface defects. Deep level transient spectroscopy (DLTS) has been used in this work to reveal information about defect levels in CuInGaSSe based solar cells. The defect spectra varied significantly from sample to sample. Majority and minority carrier traps were identified for each cell. An effort was made to correlate the traps with the chemical nature of defects. In particular, cells were investigated that had three different buffer layers namely CdS, ZnO and ZnS. In the case of ZnO and ZnS buffer layer devices cells with high and low efficiencies were studied. The lower efficiency cells were characterized by deeper trap levels. PACS: 84.60.Jt; 71.20.Nr
2006. "Fast Multipole Methods for Particle Dynamics." Molecular Simulation 32(10-11):775-790. doi:10.1080/08927020600991161 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. The growth of simulations of particle systems has been aided by advances in computer speed and algorithms. The adoption of O(N) algorithms to solve N-body simulation problems has been less rapid due to the fact that such scaling was only competitive for relatively large N. Our work seeks to find algorithmic modifications and practical implementations for intermediate values of N in typical use for molecular simulations. This article reviews fast multipole techniques for calculation of electrostatic interactions in molecular systems. The basic mathematics behind fast summations applied to long ranged forces is presented along with advanced techniques for accelerating the solution, including our most recent developments. The computational efficiency of the new methods facilitates both simulations of large systems as well as longer and therefore more realistic simulations of smaller systems.
2006. "A New Class of Highly Dispersed VOx Catalysts on Mesoporous Silica: Synthesis, Characterization, and Catalytic Activity in the Partial Oxidation of Ethanol." Applied Catalysis. A, General 300(2):109-119. Abstract The morphology of vanadium oxide supported on a titania-modified mesoporous silica (MCM-41), obtained by means of a careful grafting process through atomic layer deposition, was studied using a variety of characterization techniques. The XRD together with TEM, 51V-NMR, Raman, FTIR and DRS-UV-Vis results showed that the vanadia species are extremely well dispersed onto the surface of the mesoporous support; the dispersion being stable upon thermal treatments up to 400 °C. Studies of the catalytic activity of these materials were performed using the partial oxidation of ethanol as a probe reaction. The results indicate an intrinsic relationship between dispersion, the presence of a TiO2-VOx phase, and catalytic activity for oxidation and dehydration.
2006. "Non-thermal plasma-assisted NOx reduction over Na-Y zeolites: The promotional effect of acid sites." Catalysis Letters 109(1-2):1-6. doi:10.1007/s10562-006-0049-3 Abstract The effect of acid sites on the catalytic activities of a series of H+-modified Na-Y zeolites was investigated in the non-thermal plasma assisted NOx reduction reaction using a simulated diesel engine exhaust gas mixture. The acid sites were formed by NH4+ ion exchange and subsequent heat treatment of a NaY zeolite. The catalytic activities of these H+-modified NaY zeolites significantly increased with the number of acid sites. This NOx conversion increase was correlated with the decrease in the amount of unreacted NO2. The increase in the number of acid sites did not change the NO level, it stayed constant. Temperature programmed desorption following NO2 adsorption showed the appearance of a high temperature desorption peak at 453 K in addition to the main desorption feature of 343 K observed for the base Na-Y. The results of both the IR and TPD experiments revealed the formation of crotonaldehyde, resulting from condensation reaction of adsorbed acetaldehyde. Strong adsorptions of both NOx and hydrocarbon species are proposed to be responsible for the higher catalytic activity of H+-modified Na-Y zeolites in comparison to the base NaY material
2006. "NOx Uptake Mechanism on Pt/BaO/Al2O3 Catalysts." Catalysis Letters 111(3-4):119-126. Abstract The NOx adsorption mechanism on Pt/BaO/Al2O3 catalysts was investigated by performing NOx storage/reduction cycles, NO2 adsorption and NO + O2 adsorption on 2%Pt/(x)BaO/Al2O3 (x = 2, 8 and 20 wt%) catalysts. NOx uptake profiles on 2%Pt/20%BaO/Al2O3 at 523 K show complete uptake behavior for almost 5 min, and then the NOx level starts gradually increasing with time and it reaches 75% of the inlet NOx concentration after 30 min time-on-stream. Although this catalyst shows fairly high NOx conversion at 523 K, only ~ 2.4 wt% out of 20 wt% BaO is converted to Ba(NO3)2. Adsorption studies by using NO2 and NO + O2 suggest two different NOx adsorption mechanisms. The NO2 uptake profile on 2%Pt/20%BaO/Al2O3 shows the absence of a complete NOx uptake period at the beginning of adsorption and the overall NOx uptake is controlled by the gas-solid equilibrium between NO2 and BaO/Ba(NO3)2 phase. When we use NO + O2, complete initial NOx uptake occurs and the time it takes to convert ~ 4 % of BaO to Ba(NO3)2 is independent of the NO concentration. These NOx uptake characteristics suggest that the NO + O2 reaction on the surface of Pt particles produces NO2 that is subsequently transferred to the neighboring BaO phase by spill over. At the beginning of the NOx uptake, this spill-over process is very fast and so it is able to provide complete NOx storage. However, the NOx uptake by this mechanism slows down as BaO in the vicinity of Pt particles are converted to Ba(NO3)2. The formation of Ba(NO3)2 around the Pt particles results in the development of a diffusion barrier for NO2, and increases the probability of NO2 desorption and consequently, the beginning of NOx slip. As NOx uptake by NO2 spill-over mechanism slows down due to the diffusion barrier formation, the rate and extent of NO2 uptake are determined by the diffusion rate of nitrate ions into the BaO bulk, which, in turn, is determined by the gas phase NO2 concentration.
