Scientific Publications 2007
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2007. "Structure and Charge Hopping Dynamics in Green Rust ." Journal of Physical Chemistry C 111(30):11414-11423. doi:10.1021/jp072762n Abstract Green rust is a family of mixed-valent iron phases formed by a number of abiotic and biotic processes under alkaline suboxic conditions. Due to its high Fe2+ content, green rust is a potentially important phase for pollution remediation by serving as a powerful electron donor for reductive transformation. However, mechanisms of oxidation of this material are poorly understood. An essential component of the green rust structure is a mixed-valent brucite-like Fe(OH)2 sheet comprised of a two dimensional network of edge-sharing iron octahedra. Room temperature Mössbauer spectra show a characteristic signature for intermediate valence on the iron atoms in this sheet, indicative of a Fe2+‑Fe3+ valence interchange reaction faster than approximately 107 s-1. Using Fe(OH)2 as structural analogue for reduced green rust, we performed Hartree-Fock calculations on periodic slab models and cluster representations to determine the structure and hopping mobility of Fe3+ hole polarons in this material, providing a first principles assessment of the Fe2+‑Fe3+ valence interchange reaction rate. The calculations show that among three possible symmetry unique iron-to-iron hops within a sheet, a hop to next-nearest neighbors at an intermediate distance of 5.6 Å is the fastest. The predicted rate is on the order of 1012 s-1 consistent the Mössbauer-based constraint. All other possibilities, including hopping across interlayer spaces, are predicted to be slower than 107 s-1. Collectively, the findings suggest the possibility of hole self-diffusion along sheets as a mechanism for regeneration of lattice Fe2+ sites, consistent with previous experimental observations of edge-inward progressive oxidation of green rust.
2007. "Electron Beam Induced Thickening of the Protective Oxide Layer around Fe Nanoparticles ." Ultramicroscopy 108(1):43-51. doi:10.1016/j.ultramic.2007.03.002 Abstract There are many circumstances in science where the process of measuring the properties of a system alters the system. An imaging process can exert an inadvertent effect on the object being observed. Consequently, what we observe does not necessarily represent what had been present before the observation. Normally this effect can be ignored if the consequence of such a change is believed not to be significant. The expansion of nanostructured materials has made high resolution transmission electron microscopy one of the indispensable tools for probing the characteristics of nano-materials. Modification of nanoparticles by the electron beam during their imaging has been widely noticed and this is generally believed to be due to electron beam induced heating effect, defect formation in the particles, charging of the particle, or excitation of surrounding gases. However, an explicit experimental identification of which process dominates is often very hard to establish. We report the thickening of native oxide layer on iron nanoparticle under electron beam irradiation. Based on atomic level imaging, electron diffraction, and computer simulation, we have direct evidence that the protecting oxide layer formed on Fe nanoparticle at room temperature in air continues to grow during an electron beam bombardment in the vacuum system typical of most TEM systems. Partial illumination of a nanoparticle and observation of the shell thickening conclusively demonstrates that many of the mechanisms postulated to explain such processes are not occurring to a significant extent. The observed growth is not related to the electron beam induced heating of the nanoparticle, or residual oxygen ionization, or establishment of an electrical field, rather it is related to electron beam facilitated mass transport across the oxide layer (a defect related process).
2007. "Morphology and Oxide Shell Structure of Iron Nanoparticles Grown by Sputter-Gas-Aggregation." Nanotechnology 18(25):Art. No. 255603. doi:10.1088/0957-4484/18/25/255603 Abstract Much recent research effort has been made on the synthesis, characterization, and property evaluation of core-shell structured Fe nanoparticles. Fundamental properties of these particles depend on both their external crystal faceting planes and the nature of a protective oxide layer. In this paper, the crystal faceting planes and oxide coating structures of core-shell structured iron/iron oxide nanoparticles synthesized by a sputter-gas-aggregation process were studied using transmission electron microscopy (TEM), electron diffraction and Wulff shape construction. The particles grown by this process and deposited on a support at room temperature process have been compared with particles grown and deposited at high temperature as reported in literature. Most synthesis processes produce round particles for particles less than 20 nm in diameter. For larger particles crystallographic facets are observed. It has been found that the Fe nanoparticles formed at RT are invariantly faceted on the {100} lattice planes and truncated by the {110} planes at different degrees. Substantial fraction of particles are confined only by the 6 {100} planes (not truncated by the {110} planes), this contrasts with the Fe particles formed at high temperature (HT) for which a predominance of {110} planes has been reported. Furthermore, at RT no particle was identified to be only confined by the 12 {110} planes which is relatively common for the particles formed at HT. The Fe cubes defined by the 6 {100} planes show a characteristic inward relaxation along the <100> and <110> directions and the reason for this behavior is not fully understood. The oxide shell on the Fe {100} plane maintains an orientation relationship: Fe(001)//Fe3O4(001) and Fe[100]//Fe3O4[110], which is same as the oxide formed on a bulk Fe(001) through thermal oxidation. Orientation of the oxide that forms on the Fe{110} facets differs from that on Fe{001}, therefore, properties of core-shell structured Fe nanoparticle faceted primarily with one type of lattice plane may be fully different from that faceted with another type of lattice planes.
2007. "Calculation of Water-Exchange Rates on Aqueous Polynuclear Clustersand at Oxide-Water Interfaces." Inorganic Chemistry 46(8):2962-2964. doi:10.1021/ic070079+ 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 rates of a wide variety of reactions in aqueous coordination compounds can be correlated with lifetimes of water molecules in the inner-coordination shell of the metal. For simple octahedral metal ions, these lifetimes span ~10²⁰ but are unknown, and experimentally inaccessible, for reactive sites in interfacial environments. Using recent data on nanometer-sized aqueous aluminum clusters, we show that lifetimes can be calculated from reactiveflux molecular dynamics simulations. Rates scale with the calculated metal-water bond lengths. Surprisingly, on all aluminum(III) mineral surface sites investigated, waters have lifetimes in the range of 10⁻⁸-10⁻power10 s, making the surface sites as fast as the most reactive ions in the solution.
2007. "Doping Golden Buckyballs: Cu@Au16- and Cu@Au17- Cluster Anions." Angewandte Chemie International Edition 46(16):2915-2918. doi:10.1002/anie.200700060 Abstract The discovery of the unique catalytic effects of gold nanoparticles on oxide substrates has stimulated a flurry of research into the structures and properties of free gold nanoclusters, which may hold the key to elucidating the catalytic mechanisms of supported gold clusters. One of the most remarkable results has been the discovery of planar gold cluster anions (Aun_) of up to twelve gold atoms and the 2D to 3D transition for clusters with n larger than 12. Among larger gold clusters, Au20 has been found to be a perfect tetrahedron. A more recent study of the structures of Aun_ cluster anions in the medium size range (n=15–19) has shown that clusters with n=16–18 possess unprecedented empty cage structures. In particular, the Au16_ cluster anion has an interesting tetrahedral structure with an inner diameter of about 5.5 0 and can be compared to the fullerenes (buckyballs). Although Au32 was first suggested to be a “24- carat golden fullerene”, subsequent studies showed that the Au32_ ion is in fact a low-symmetry compact 3D structure. Other larger gold cage clusters have also been proposed computationally, but none has been observed or is expected to be the global minimum. The cage structures of the cluster anions Au16_ and Au17_ have recently been confirmed by electron diffraction and thus they are the first experimentally confirmed and the smallest possible gold cages. The large empty space inside these cage clusters immediately suggested that they can be doped with a foreign atom to produce a new class of endohedral gold cages analogous to endohedral fullerenes.
2007. "Doping the Golden Cage Au16- with Si, Ge, and Sn." Journal of the American Chemical Society 129(49):15136-15137. doi:10.1021/ja077465a Abstract The discovery of catalytic effects in gold nanoparticles1 has accelerated efforts on the characterization and understanding of the structures and properties of bare gold clusters.2,3 Doped gold clusters have received increasing attention because of their potential tunable catalytic properties vs. dopant. The first highly stable doped gold cluster was a closed-shell icosahedral W@Au12, predicted using density-functional theory (DFT) by Pyykkö and Runeberg4 and confirmed using photoelectron spectroscopy (PES) by Li et al5. Subsequent PES studies showed that V-, Nb-, and Ta-doped Au12 clusters also possess the Ih symmetry.6 Mass spectra of a number of Au-alloy clusters have been observed by Lievens and co-workers.
2007. "CB7-: Experimental and Theoretical Evidence Against Hypercoordinated Planar Carbon." Angewandte Chemie International Edition 46(24):4550-4553. Abstract The B82– cluster was previously shown to possess a planar molecular wheel structure with a heptacoordinated boron. Substitution of one B– by C in B82– is expected to yield a closed shell CB7– molecular wheel, which has been produced experimentally in a cluster beam and probed by photoelectron spectroscopy. Ab initio calculations show that the CB7– cluster possesses an extremely stable planar C2v structure, in which the C atom substitutes a B– atom at the edge of the B82– molecular wheel, whereas the D7h structure with a heptacoordinated C is a high-lying isomer 63.2 kcal/mol (CCSD(T)/6-311+G(2df)//CCSD(T)/6-311+G*) above the global minimum. The combined experimental and ab initio study demonstrates that a heptacoordinated planar carbon in CB7– is extremely unfavorable and is not a viable candidate for experimental realization of hypercoordinated planar carbon molecules.
2007. "Covalent Immobilization of Peptides on Self-Assembled Monolayer Surfaces Using Soft-Landing of Mass-Selected Ions." Journal of the American Chemical Society 129:8682-8683. Abstract Covalent immobilization of peptides on solid supports plays an important role in biochemistry with applications ranging from characterization of molecular recognition events at the amino acid level and identification of biologically active motifs in proteins to development of novel biosensors and substrates for improved cell adhesion. Self-assembled monolayer surfaces (SAMs) provide a simple and convenient platform for tailoring chemical properties of a variety of substrates. Existing techniques for linking peptides to SAMs are based on solution-phase synthetic strategies and require relatively large quantities of purified material. Here, we report a novel approach for highly selective covalent binding of peptides to SAMs using soft-landing (SL) of mass-selected ions. SL is defined as intact deposition of ions onto suitable substrates at hyperthermal (<100 eV) energies.Recent studies have demonstrated that SAMs are excellent deposition targets for SL due to their ability to dissipate kinetic energies of the projectiles and their efficiency in trapping captured species. It has been proposed that SL could be utilized for controlled preparation of protein arrays.
2007. "Photoelectron Spectroscopy of Singly and Doubly Charged Higher Fullerenes at Low Temperatures: C76-, C78-, C84- and C76(2-), C78(2-), C84(2-) ." Journal of Physical Chemistry C 111(48):17684-17689. Abstract Photoelectron spectroscopy of vibrationally cold singly and doubly charged higher fullerenes, Cn– and Cn2– (n = 76, 78, and 84), has been investigated at several photon energies. Vibrationally resolved spectra are obtained for both the singly and doubly charged species and for n = 78 and 84 transitions from different isomers are also observed. The electron affinities (EA’s) of C76, C78, and C84 are accurately determined to be 2.975±0.010 eV for C76, 3.20±0.01 eV for C78(C2v), 3.165±0.010 eV for C78(D3), 3.23±0.02 for C78(C2v’), 3.185±0.010 eV for C84(D2), and 3.26±0.02 eV for C84(D2d). The second EA’s of the higher fullerenes, which represent the electronic stability of the doubly charged anions, are measured to be 0.325±0.010 eV for C76, 0.44±0.02 eV for C78(C2v), 0.53±0.02 eV for C78(D3), 0.60±0.04 eV for C78(C2v’), 0.615±0.010 eV for C84(D2d), and 0.82±0.01 eV for C84(D2). The spectra of the dianions are observed to be similar to that of the singly charged anions, suggesting that the charging induces relatively small structural changes to the fullerene cages. The onsite Coulomb repulsions in the doubly charged fullerenes are directly measured from the differences of the first and second EA’s and reveal strong correlation effects between the two extra electrons. The repulsive Coulomb barriers in the doubly charged fullerenes are estimated from the cutoff in the photoelectron spectra and are found to be consistent with estimates from an electrostatic model.
2007. "Preface." Catalysis Today 120(1):1. Abstract The 19th North American Catalysis Society Meeting (19 NAM) was held on May 22–27, 2005 in Philadelphia, Pennsylvania, USA. NAM meetings are held every 2 years and are hosted by one of the 14 local Catalysis Clubs in the United States, Canada, and Mexico. The Novel Compact Catalytic Reactor session was organized as part of the 19 NAM meeting to promote and disseminate knowledge in the field of novel reactor and reaction engineering. The session included three keynote lectures, nine oral presentations, and 19 posters. The topics of these presentations covered current research activities in novel reactor design, microreactors for catalyst discovery, compact reactors for energy generation and chemical processing, and reactor miniaturization. The contributions to this session provide the basis for this special issue of Catalysis Today. Several, additional papers submitted at the request of the Guest Editors are also included in this issue.We wish to express our appreciation to the keynote speakers, Professor Klavs Jensen (MIT, USA), Dr Volker Hessel (IMM, Germany), and Dr. Anna Lee Tonkovich (Velocys, USA) for their valuable contributions. We are grateful to the reviewers for their cooperation and in-depth comments made to the submitted manuscripts. We gratefully acknowledge Professor Jerry Spivey, the Associate Editor of this journal, for his valuable advice. Finally, we would like to thank all of the authors for contributing original papers to this issue.
2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104(20):8328-8333. doi:10.1073/pnas.0701103104 Abstract While directional movement requires morphological polarization characterized by formation of a leading pseudopodium at the front and a trailing rear at the back, little is known about how protein networks are spatially integrated to regulate this process. Here, we utilize a unique pseudopodial purification system and quantitative proteomics and phosphoproteomics to map the spatial relationship of 3509 proteins and 228 distinct sites of phosphorylation in polarized cells. Networks of signaling proteins, metabolic pathways, actin regulatory proteins, and kinase-substrate cascades were found to partition to different poles of the cell including components of the Ras/ERK pathway. Also, several novel proteins were found to be differentially phosphorylated at the front or rear of polarized cells and to localize to distinct subcellular structures. Our findings provide insight into the spatial organization of signaling networks that control cell movement and provide a comprehensive profile of proteins and their sites of phosphorylation that control cell polarization.
2007. "Thermal Conductivity of GaN Nanotubes Simulated by Nonequilibrium Molecular Dynamics." Physical Review. B, Condensed Matter 75(12):Art. No. 153303. doi:10.1103/PhysRevB.75.153303 Abstract Thermal conductivity of GaN nanotubes along the tube axis is investigated over the temperature range of 600K-2300K using homogeneous nonequilibrium molecular dynamics. In general, the thermal conductivity of nanotubes is smaller than that for the bulk GaN single crystal. The thermal conductivity is also found to decrease with temperature and increase with increasing wall thickness of the nanotubes. The change of phonon spectrum and surface inelastic scattering may account for the reduction of thermal conductivity in the nanotubes, while thermal softening and high frequency phonon interactions at high temperatures may provide an explanation for its decrease with increasing temperature.
2007. "Carbon Nanotubes Grow on the C Face of SiC (0001) during Sublimation Decomposition:Quantum Chemical Molecular Dynamics Simulations." Journal of Physical Chemistry C 111(35):12960-12972. doi:10.1021/jp072208d 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. High-temperature quantum chemical molecular dynamics simulations (QM/MD) based on the density functional tight binding (DFTB) method were performed on SiC surfaces and compared with experimental observations. Following the nucleation of nanocaps on the C face of SiC(0001), substantial carbon nanotube (CNT) growth is observed during evaporation of Si between 2000 and 3000 K, while the Si face appears not capable of nanocap formation and perpendicular tube growth under otherwise identical conditions. Instead, graphene sheet growth parallel to the surface is observed in this case. Si evaporation is modeled by two approaches to Si atom removal, one where all Si atoms in one surface layer are removed simultaneously and another one where Si atoms are individually removed from random positions in selected surface layers. The tubes directly “grown” in our simulations display many sidewall defects, consistent with experimental findings. During random removal of Si on the C face, we also observe first indications for growth of a second inner tube, and we observe buildup of amorphous carbon around the tube/surface interface. The present simulations provide atomic-level, time-resolved insight into the interactions of graphitic material on SiC surfaces in the 100 ps domain. Analysis of our simulations under consideration of the geometry of the SiC lattice allows qualitative understanding of the origins for different carbon growth modes, namely, perpendicular tube growth on the C face and parallel slab growth on the Si face.
2007. "Atomistic Study of the Melting Behavior of Single Crystalline Wurtzite Gallium Nitride Nanowires." Journal of Materials Research 22(3):742-747. doi:10.1557/JMR.2007.0095 Abstract Molecular dynamics (MD) simulation was used to study the melting behavior of GaN nanowires with Stillinger-Webber (SW) potential. Our results reveal that the melting of nanowires starts from the surface, and rapidly extends to the inner regions of nanowires as temperature increases. The melting temperature of GaN nanowires is lower than that of the bulk GaN, which may associate with large surfaces of nanowires. The melting temperatures increase to saturation values ~3100K and ~2900K when the diameters of nanowires are larger than 3.14 and 4.14 nm for nanowires with [100]- and [110]-oriented lateral facets, respectively.
2007. "Size dependence of melting of GaN nanowires with triangular cross sections." Journal of Applied Physics 101(4):043511. doi:10.1063/1.2512140 Abstract Molecular dynamics simulations have been used to study the melting of GaN nanowires with triangular cross-sections. The curve of the potential energy, along with the atomic configuration is used to monitor the phase transition. The thermal stability of GaN nanowires is dependent on the size of the nanowires. The melting temperature of the GaN nanowires increases with the increasing of area cross-section of the nanowires to a saturation value. An interesting result is that of the nanowires start to melt from the edges, then the surface, and extends to the inner regions of nanowires as temperature increases.
2007. "Atomistic Simulation of the Size and Orientation Dependences of Thermal Conductivity in GaN Nanowires." Applied Physics Letters 90(16):Art. No. 161923. doi:10.1063/1.2730747 Abstract The thermal conductivity of GaN nanowires has been determined computationally, by applying nonequilibrium atomistic simulation methods using the Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] potentials. The simulation results show that the thermal conductivity of the GaN nanowires is smaller than that of a bulk crystal and increases with increasing diameter. Surface scattering of phonons and the high surface to volume ratios of the nanowires are primarily responsible for the reduced thermal conductivity and its size dependence behavior. The thermal conductivity is also found to decrease with increasing temperature, which is due to phonon-phonon interactions at high temperatures. The thermal conductivity also exhibits a dependence on axial orientation of the nanowires.
2007. "Atomistic Simulations of the Size, Orientation and Temperature Dependence of Tensile Behavior in GaN Nanowires." Physical Review. B, Condensed Matter and Materials Physics 76(4):Art. No. 045310. doi:10.1103/PhysRevB.76.045310 Abstract Molecular dynamics simulations with Stillinger-Weber potentials were used to study the response of wurtzite-type single crystalline GaN nanowires to a tensile strain along the axial direction. Nanowires with axial orientations along the [0001], [1 00] and [11 0] crystallographic directions, which correspond to experimentally synthesized nanowires, were studied. The results reveal that the nanowires with different axial orientations show distinctly different deformation behavior under loading. The brittle to ductile transition (BDT) was observed in the nanowires oriented along the [0001] direction and the BDT temperatures lie in the temperature range between 1500 and 1800 K. The nanowires oriented along the [11 0] direction exhibit slip in the {01 0} planes; whereas the nanowires oriented along the [1 00] direction fracture in a cleavage manner under tensile loading. It should be emphasized that multiple yield stresses were observed during different stages in the [11 0]-oriented nanowires. In general, Young's modulus of the GaN nanowires decreases with decreasing diameter of the nanowires.
2007. "Effective Hydraulic Properties Determined from Transient Unsaturated Flow in Anisotropic Soils." Vadose Zone Journal 6(4):913-924. doi:10.2136/vzj2006.0174 Abstract Hydraulic parameters including the pore connectivity/tortuosity tensor (L_i) were inversely estimated using the STOMP numerical simulator coupled with the parameter estimation code, UCODE. Results show that six of eight parameters required for a modified van Genuchten-Mualem model could be inversely estimated using water content measured during transient infiltration from a surface line source and approximated prior information. Soils showed evidence of saturation-dependent anisotropy that was well described with the connectivity tensor. Variability of the vertical saturated hydraulic conductivity was larger than the horizontal. The autocorrelation ranges for the horizonatal and vertical Ks; the inverse of the air-entry value, and the horizontal connectivity were between 2.4 and 4.6 m whereas the van Genuchten shape parameter, n, and saturated water content showed no autocorrelation. Accurate upscaling of hydraulic properties requires the correct assessment of the connectivity of facies.
2007. "Electroscopy Ionization Photoelectron Spectroscopy: Probing the Electronic Structure of Inorganic Metal Complexes in the Gas Phase." Coordination Chemistry Reviews 251(3-4):474-491. Abstract The coupling of electrospray to photoelectron spectroscopy has allowed a number of negatively charged solution phase transition metal complexes to be transferred to the gas phase and studied by photoelectron spectroscopy for the first time. Experiments have been performed on a range of species, including classic square-planar and octahedral transition-metal halide complexes, metal-metal bonded species, transition metal bis(dithiolene) centers and a variety of mononuclear and polynuclear iron-sulfur clusters that are related to important bioinorganic centers. The studies have provided detailed information about the electronic structure and molecular orbital energy levels of these species, allowing for direct comparison with theoretical calculations, and providing insight into their intrinsic redox properties in the absence of solvation.
2007. "Current Trends in Computational Inference from Mass Spectrometry-based Proteomics." Briefings in Bioinformatics 8(5):304-317. doi:10.1093/bib/bbm023 Abstract Mass spectrometry offers a high-throughput approach to quantifying the proteome associated with a biological sample and hence has become the primary approach of proteomic analyses. Computation is tightly coupled to this advanced technological platform as a required component of not only peptide and protein identification, but quantification and functional inference, such as protein modifications and interactions. Proteomics faces several key computational challenges such as identification of proteins and peptides from tandem mass spectra as well as their quantitation. In addition, the application of proteomics to systems biology requires understanding the functional proteome including how the dynamics of the cell change in response to protein modifications and complex interactions between biomolecules. This review presents an overview of recently developed methods and their impact on these core computational challenges currently facing proteomics.
2007. "Possible Regulatory Role for the Histidine-Rich Loop in the Zinc Transport Protein, ZnuA." Biochemistry 46(30):8734-8743. doi:10.1021/bi700763w Abstract A number of bacterial metal transporters belong to the ABC transporter family. To better understand the structural determinants of metal selectivity of one such transporter, we previously determined the structure of the periplasmic domain of a zinc transporter, ZnuA, from Synechocystis 6803 and determined that ZnuA binds zinc via three histidines. Unique to these ABC zinc transporters, ZnuA has a highly charged and mobile loop that protrudes from the protein in the vicinity of the metal binding site that we had suggested might facilitate zinc acquisition. To further examine the function of this loop, the structure and zinc binding properties of two ZnuA variants were determined. When the loop is entirely deleted, zinc still binds to the three histidines. However, unlike what was suggested from the structure of a similar solute binding protein, TroA, release of zinc occurs concomitantly with large conformational changes in two of the three chelating histidines. These structural results combined with isothermal titration calorimetry data demonstrates that there are at least two classes of zinc binding sites; the high affinity site in the cleft between the two domains and at least one additional site on the flexible loop. This loop has approximately 100-fold weaker affinity for zinc than the high affinity zinc binding site and its deletion does not affect the high affinity site. From these results, we suggest that this region might be a sensor for high periplasmic levels of zinc.
2007. "Study of Copper Diffusion Through Ruthenium Thin Film by Photoemission Electron Microscopy." Applied Physics Letters 90:111906. doi:10.1063/1.2712832 Abstract Photoemission electron microscopy (PEEM) is employed to study Cu diffusion in real time through a Ru barrier in a Cu/Ru bilayer system. The PEEM images display large contrast between Cu and Ru due of the differences in work function between the two metals, making PEEM an ideal methodology to study diffusion in real time. At low temperature (175-290 °C), Cu mainly diffuses through the defective sites in the Ru film. Uniform diffusion of Cu through a Ru thin film occurs at approximately 300 °C. The results are confirmed by X-ray photoemission spectroscopy (XPS) depth profiling and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS) analysis.
2007. "Molecular Dynamics Simulations of Trichomonas vaginalis FerredoxinShow a Loop-Cap Transition." Biophysical Journal 92:3337-3345. doi:10.1529/biophysj.106.088096 Abstract The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2A˚ . However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.
2007. "Molecular Dynamics Simulations of Trichomonas vaginalis FerredoxinShow a Loop-Cap Transition." Biophysical Journal 92(10):3337-3345. doi:10.1529/biophysj.106.088096 Abstract The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2A˚ . However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.
2007. "Efficacy of soluble sodium tripolyphosphate amendments for the in-situ immobilisation of uranium." Environmental Chemistry 4:293-300. doi:10.1071/EN07030 Abstract A series of conventional saturated and pressurized unsaturated flow (PUF) column experiments were conducted to evaluate the effects of utilizing soluble polyphosphate amendments for in situ, subsurface remediation of uranium. Experiments were conducted under mildly alkaline, calcareous conditions, representative of conditions commonly encountered at sites across the arid western United States. Results presented here illustrate that application of a soluble polyphosphate amendment to sediment contaminated with uranium will rapidly reduce the concentration of uranium to near or below drinking water limits under water saturated and unsaturated conditions. Column experiment conducted in the absence of polyphosphate illustrate sustained release of aqueous uranium at concentrations well above drinking water standards in excess of over 25 pore volumes under saturated conditions and over 50 pore volumes under water unsaturated conditions. However, in the presence of tripolyphosphate the concentration of aqueous uranium released from sediment was near or below drinking water limits within 10 to 35 pore volumes under saturated and unsaturated conditions, respectively. Moreover, results indicate the necessity of conducting site specific dynamic tests in order to tailor phosphate remediation technology based relevant geochemical and hydrological conditions.
2007. "Experimental Limitations Regarding the Formation and Characterization of Uranium-Mineral Phases in Concrete Waste Forms." Cement and Concrete Research 37(2):151-160. Abstract Predicting the long-term fate of low-level radioactive waste forms requires understanding how the radionuclides interact with the waste form. Concrete encasement is one method being considered for containment of low-level radioactive wastes. The necessary data to conduct an accurate performance assessment of such a waste form requires understanding the behavior and interactions of the radionuclides with the concrete matrix. The formation of uranium mineral phases has been investigated in simulated concrete pore fluids and Ordinary Portland Cement/Pulverized Fuel Ash (fly ash) concrete waste forms. X-Ray diffraction analyses of uranium precipitates from concrete pore fluids suggest diuranate salts, uranium-oxyhydroxides, and –silicates as solubility limiting phases. Scanning electron microscopy – energy dispersive spectroscopic analyses of uranium-spiked concrete suggests that under conditions both under-saturated and over-saturated with respect to the formation of uranium mineral phases, uranyl-oxyhydroxide phases precipitate within the initial two weeks. Subsequently, uranyl-silicate phases form after approximately one month and uranyl-phosphate phases provide a significant contribution to the long-term control over uranium in concrete waste forms after two months. This investigation demonstrates the importance of investigating the solubility of complex contaminants such as uranium in the complete matrix (i.e. concrete matrix versus pore fluids) and suggests the importance of secondary uranium mineral phases in the long-term retention within concrete waste forms.
2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6(2):828-836. doi:10.1021/pr0604920 Abstract Multiple approaches for simplifying the serum proteome have been described. These techniques are generally developed across different laboratories, samples, mass spectrometry platforms, and analysis tools. Hence, comparing the available schemes is impossible from the existing literature because of confounding variables. We describe a head-to-head comparison of several serum fractionation schemes, including N-linked glycopeptide enrichment, cysteinyl-peptide enrichment, magnetic bead separation (C3, C8, and WCX), size fractionation, Protein A/G depletion, and immunoaffinity column depletion of abundant serum proteins. Each technique was compared to results obtained from unfractionated human serum. The results show immunoaffinity subtraction is the most effective means for simplifying the serum proteome and maintaining reasonable sample throughput. The reported dataset is publicly available and provides a standard against which emergent technologies can be compared and evaluated for their contribution to serum-based biomarker discovery.
2007. "Mechanisms of Electron Transfer in Two Decaheme Cytochromes from a Metal-Reducing Bacterium." Journal of Physical Chemistry B 111(44):12857-12864. doi:10.1021/jp0718698 Abstract Single-molecule current-voltage (I–V) spectra were collected using a scanning tunneling microscope for two decaheme c-type cytochromes, OmcA and MtrC, which are outer-membrane proteins from the dissimilatory metal-reducing bacterium Shewanella oneidensis. Although the two cytochromes are similar in heme count, charge-carrying amino-acid content, and molecular mass, their I–V spectra are significantly different. The I–V spectra for OmcA show smoothly varying symmetric exponential behavior. These spectra are well fit by a coherent tunneling model that is based on a simple square barrier description of the tunneling junction. In contrast, the I–V spectra for MtrC have pronounced breaks in slope in the positive tip bias range. Two large peaks in the normalized differential conductance spectra of MtrC were fit to a tunneling model that accounts for the possibility of transient population of empty states stabilized by vibrational relaxation. Reorganization energies deduced for the two features are similar to those normally assigned to metal centers in other metalloproteins. Work function measurements of the cytochrome films were used to convert the energies of these two spectral features to the normal hydrogen electrode scale for comparison with the midpoint potential measured using protein film voltammetry, which showed good correspondence. We conclude that MtrC mediates tunneling current by heme orbital participation. The difference in tunneling behavior between OmcA and MtrC suggests distinct physiological functions for the two cytochromes; in contrast to OmcA, MtrC appears to be tuned to a specific operating potential.
2007. "Relative Raman Intensities in C6H6, C6D6, and C6F6: A Comparison of Different Computational Methods." Theoretical Chemistry Accounts 117(2):283-290. doi:10.1007/s00214-006-1350-z Abstract In order to determine which models can best emulate Raman spectra, the accuracy of various computational methods (Hartee-Fock, MP2, CCSD, CAS-SCF, and several types of DFT) for predicting relative intensities in the Raman spectra of C6H6, C6D6, and C6F6 were compared. In particular, the predicted relative intensities for v1 and v2 were compared with relative intensities measured by an FT-Raman spectrometer. While none of these methods excelled at this prediction, Hartee-Fock with a large basis set was most successful for C6H6, and C6D6, while PW91PW91 with the aug-cc-pVTZ basis set was most successful for C6F6.
2007. "Electrochemical Effects of S Accumulation on Ion-implanted Alloy 22 in 1 M NaCl Solutions." Corrosion Science 49(6):2497-2511. doi:10.1016/j.corsci.2006.12.003 Abstract The objective of this study was to examine the effects of high levels of S in the near-surface region on the passivity of Alloy 22, a corrosion resistant Ni-Cr-Mo alloy, in deaerated 1 M NaCl solution. Near-surface concentrations of S up to 2 at.% were achieved in Alloy 22 test specimens by implanting them with S. The S-implanted samples were then evaluated in short-term electrochemical tests in the salt solution and subsequently analyzed with X-ray Photoelectron Spectroscopy (XPS) for film thickness and composition. Specimens tested included non-implanted and annealed Alloy 22 samples, samples implanted with S, and “blanks” implanted with Ar as an ion that would simulate the “damage” of S implantation without the chemical effect. A sample of S-implanted Alloy 22 was also exposed to solution for 29 days and analyzed for evidence of S accumulation at the surface over longer times
2007. "Angle-dependent Study of a Direct Optical Transition in the sp Bands of Ag(111)by One- and Two-photon Photoemission." Physical Review. B, Condensed Matter 76:195428 1-11. doi:10.1103/PhysRevB.76.195428 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 have measured angle-dependent photoemission spectra for one-photon and two-photon excitation from Ag(111). The observed dispersion of the sp-band transition of Ag(111) can be reproduced using a nearly-freeelectron model for the initial and final states involved. The observed dispersion agrees with the known band structure. We illustrate how the strong refraction of low-energy electrons becomes a limiting factor to obtain quantitative band-structure information. Conversely, low-energy electrons of a well-defined direct optical interband transition can provide a sensitive probe of the inner potential. We observe asymmetric two-photon photoelectron intensity distributions with respect to detection along the surface normal. These intensity distributions can be well described by a phenomenological model which employs the Fresnel equations to calculate the electric field components of the incident radiation inside the sample. Very good agreement is found using tabulated optical constants and a momentum matrix element, which is oriented along the surface normal. In contrast, the observed intensity distribution for one-photon photoemission from Ag(111) does not fit the simple Fresnel model. We interpret this as the influence of surface photoemission. By comparison to Cu(001), we show that the expected intensity distributions of the Fresnel model for one-photon photoemission and twophoton photoemission are valid for an orientation of the momentum matrix element along the surface normal if the influence of additional effects like surface photoemission can be neglected.
2007. "Quantum-Dots Based Electrochemical Immunoassay of Interleukin-1α." Electrochemistry Communications 9(7):1573-1577. doi:10.1016/j.elecom.2007.02.024 Abstract We describe a quantum-dot (QD, CdSe@ZnS)-based electrochemical immunoassay to detect a protein biomarker, interleukin-1α (IL-1α). QD conjugated with anti-IL-1α antibody was used as a label in an immunorecognition event. After a complete sandwich immunoreaction among the primary IL-1α antibody (immobilized on the avidin-modified magnetic beads), IL-1α, and the QD-labeled secondary antibody, QD labels were attached to the magnetic-bead surface through the antibody-antigen immunocomplex. Electrochemical stripping analysis of the captured QDs was used to quantify the concentration of IL-1α after an acid-dissolution step. The streptavidin-modified magnetic beads and the magnetic separation platform were used to integrate a facile antibody immobilization (through a biotin/streptavidin interaction) with immunoreactions and the isolation of immunocomplexes from reaction solutions in the assay. The voltammetric response is highly linear over the range of 0.5 to 50 ng mL-1 IL 1α, and the limit of detection is estimated to be 0.3 ng mL-1 (18 pM). This QD-based electrochemical immunoassay shows great promise for rapid, simple, and cost-effective analysis of protein biomarkers.
