Scientific Publications 2006
2006. "Multivariate Curve Resolution Applied to Infrared Reflection Measurements of Soil Contaminated with an Organophosphorus Analyte." Applied Spectroscopy 60(7):713-722. doi:10.1366/000370206777887026 Abstract Multivariate curve resolution (MCR) is a powerful technique for extracting chemical information from measured spectra on complex mixtures. The difficulty with applying MCR to soil reflectance measurements is that light scattering artifacts can contribute much more variance to the measurements than the analyte(s) of interest. Two methods were integrated into a MCR decomposition to account for light scattering effects. Firstly, an extended mixture model using pure analyte spectra augmented with scattering ‘spectra’ was used for the measured spectra. And secondly, second derivative preprocessed spectra, which have higher selectivity than the unprocessed spectra, were included in a second block as a part of the decomposition. The conventional alternating least squares (ALS) algorithm was modified to simultaneously decompose the measured and second derivative spectra in a two-block decomposition. Equality constraints were also included to incorporate information about sampling conditions. The result was an MCR decomposition that provided interpretable spectra from soil reflectance measurements.
2006. "Atomic-Level Simulation of Epitaxial Recrystallization and Phase Transformation in SiC." Journal of Materials Research 21(6):1420-1426. doi:10.1557/JMR.2006.0176 Abstract A nano-sized amorphous layer embedded in a perfect crystal has been created to study the amorphous-to-crystalline (a-c) transition and subsequent phase transformation in 3C-SiC by means of classical molecular dynamics methods. The recovery of bond defects and the rearrangement of atoms at the interfaces are important processes driving the initial epitaxial recrystallization of the amorphous layer, which is eventually hindered by the nucleation and growth of a polycrystalline 2H-SiC phase. A spectrum of activation energies, ranging from about 0.8 eV to 2.0 eV, is associated with these processes. Following formation of the 2H phase, the kink sites and triple junctions formed at the interfaces between 2H- and 3C-SiC provide low-energy paths for 2H-SiC atoms to transform to 3C-SiC atoms, and complete recrystallization back to the 3C structure occurs at 2000 K with an activation energy on the order of 2.3 eV.
2006. "Atomic-Level Simulations of Epitaxial Recrystallization and Amorphous-to-Crystalline Transition in 4H-SiC." Physical Review. B, Condensed Matter 74(10):104108, 1-9. doi:10.1103/PhysRevB.74.104108 Abstract The amorphous-to-crystalline (a-c) transition in 4H-SiC has been studied using molecular dynamics (MD) methods, with simulation times of up to a few hundred ns and at temperatures ranging from 1000 to 2000 K. Two nano-sized amorphous layers, one with the normal of a-c interfaces along the [ -12-10] direction and the other along the [ -1010] direction, were created within a crystalline cell to study expitaxial recrystallization and the formation of secondary phases. The recovery of bond defects at the interfaces is an important process driving the epitaxial recrystallization of the amorphous layers. The amorphous layer with the a-c interface normal along the [-12-10] direction can be completely recrystallized at the temperatures of 1500 and 2000 K, but the recrystallized region is defected with dislocations and stacking faults. On the other hand, the recrystallization process for the a-c interface normal along [-1010] direction is hindered by the nucleation of polycrystalline phases, and these secondary ordered phases are stable for longer simulation times. A general method to calculate activation energy spectra is employed to analyze the MD annealing simulations, and the recrystallization mechanism in SiC consists of multiple stages with activation energies ranging from 0.8 to 1.7 eV.
2006. "Development of Partial-Charge Potential for GaN." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 250(1-2):50-53. doi:10.1016/j.nimb.2006.04.082 Abstract Partial-charged potentials for GaN are systematically developed that describes a wide range of structural properties, where the reference data for fitting the potential parameters are taken from ab initial calculations or experiments. The present potential model provides a good fit to different structural geometries and high pressure phases of GaN. The high-pressure transition from wurtzite to rock-salt structure is correctly described yielding the phase transition pressure of about 55 GPa, and the calculated volume change at the transition is in good agreement with experimental data. The results are compared with those obtained by ab initio simulations.
2006. "Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean ." International Journal of Systematic and Evolutionary Microbiology 56(8):1911-1916. Abstract A novel marine bacterial strain, PV-4T, isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0–42 °C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4T was iso-C15 : 0. Strain PV-4T had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4T within the genus Shewanella. PV-4T exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4T showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4T (=ATCC BAA-1088T=DSM 17748T).
2006. "Molecular simulations of the transport of molecules across the liquid/vapor interface of water." Chemical Reviews 106(4):1355-1374. Abstract The transport of molecules across the liquid/vapor interface of water is a fundamental process that is important in a number of areas. Uptake of trace molecules by aqueous droplets is important in the atmosphere as it enables heterogeneous new chemical pathways that are not available in the gas phase. The uptake of molecules by water and partitioning to the air/water surface is important in aquatic environmental systems. The summary of molecular simulations presented in this work supports a picture of solute transport across the water’s vapor/liquid interface in which a hydrophilic solute molecule impinging on the surface is rapidly equilibrated, sticks to the surface of the interface with nearly unit probability, then diffuses into the bulk liquid on an free energy surface. Analysis of a large number of experimental observations of uptake, using a variety of techniques, supports a view of mass transport that is diametrically opposed – most solute molecules that collide with the surface return to the vapor rather than being absorbed into the liquid. This discrepancy stresses the need for greater understanding of the important process of uptake. We provide a perspective on molecular-scale simulations and evaluate the type of accuracy we should expect for interfacial properties, particularly those associated with the update of molecular at the surface. We briefly review computational methods commonly used in studies of aqueous interfaces, including functional forms of the molecular interaction potentials, descriptions of the simulation methodologies, and descriptions of the molecular models of the interface. We present the results of simulations of select properties of the air/water interface and properties of molecular interactions at interfaces and present an overview of modeling approaches to the macroscopic process of uptake. In particular, we present detailed descriptions of the uptake process in flow tube experiments with the help of fluid dynamics calculations toward critical comparison between the uptake experiments and the molecular simulations.
2006. "Impact of Cloud-Borne Aerosol Representation on Aerosol Direct and Indirect Effects." Atmospheric Chemistry and Physics 6:4163-4174. Abstract Aerosol particles attached to cloud droplets are much more likely to be removed from the atmosphere and are much less efficient at scattering sunlight than if unattached. Models used to estimate direct and indirect effects of aerosols employ a variety of representations of such cloud-borne particles. Here we use a global aerosol model with a relatively complete treatment of cloud-borne particles to estimate the sensitivity of simulated aerosol, cloud and radiation fields to various approximations to the representation of cloud-borne particles. We find that neglecting transport of cloud-borne particles introduces little error, but that diagnosing cloud-borne particles produces global mean biases of 20% and local errors of up to 40% for many variables of interest. A treatment that predicts the total mass concentration of cloud-borne particles for each mode yields smaller errors and runs 20% faster than the complete treatment.
2006. "Bond Length and Local Energy Density Property Connections for Non-transition- Metal-Oxide-Bonded Interactions." Journal of Physical Chemistry A 110(44):12259-12266. doi:10.1021/jp062992m Abstract For a variety of molecules and Earth materials, the theoretical local kinetic energy density, G(rc), increases and the local potential energy density, V(rc), decreases as the MO bond lengths (M = first and second row metal atoms) decrease and electron density, ρ(rc), is localized at the bond critical points, rc. Despite claims that the ratio, G(rc)/ρ(rc), classifies bonded interactions as shared covalent when less than unity and closed shell ionic when greater than unity, the ratio was found to increase from 0.5 to 2.5 a.u. as the local electronic energy density H(rc) = G(rc) + V(rc) decreases and becomes progressively more negative. In any event, the ratio is indicated to be a measure of the character for a given M-O bond, the greater the ratio, the larger the value of ρ(rc), the smaller the coordination number of the M atom and the more covalent the bond. H(rc)/ρ(rc) vs. G(rc)/ρ(rc) scatter diagrams categorize the M-O bond data into domains with the H(rc)/ρ(rc) ratio tending to increase as the electronegativity of the M atoms increase. Estimated values of G(rc) and V(rc), using an expression based on gradient corrected electron gas theory, are in good agreement with theoretical values, particularly for bonded interactions involving second row M atoms. The agreement is poorer for the more covalent C-O and N-O bonds.
2006. "Si-O Bonded Interactions in Silicate Crystals and Molecules: A Comparison." Journal of Physical Chemistry A 110(46):12678 (6 pages). Abstract Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, ρ(r), calculated for silicates like quartz and molecules like disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in crystals are short-ranged and molecular-like. Using the G(rc)/ρ(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc) = G(rc) + V(rc), and the oordination number of the Si atom decrease, and as the value of the electron density at the bond critical point, ρ(rc) and the Laplacian, ∇2ρ(rc), increase. The G(rc)/ρ(rc) and H(rc)/ρ(rc) ratios categorize the bond as observed for other second row atom M-O bonds into nonequivalent classes with the covalent character of each of the M-O bonds increasing with the H(rc)/ρ(rc) ratio. Some workers consider the Si-O bond to be highly ionic and others considered it to be either intermediate or substantially covalent. The character of the bond is examined in terms of the large net atomic basin charges conferred on the Si atoms comprising disiloxane, stishovite, quartz and forsterite, the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is intermediate in character between Al-O and P-O bonded interations rather than being ionic or covalent.
2006. "A Solid-State NMR Study of the Dynamics and Interactions ofPhenylalanine Rings in a Statherin Fragment Bound toHydroxyapatite Crystals." Journal of the American Chemical Society 128(16):5364-5370. doi:10.1021/ja056731m Abstract Extracellular matrix proteins regulate hard tissue growth by acting as adhesion sites for cells, by triggering cell signaling pathways, and by directly regulating the primary and/or secondary crystallization of hydroxyapatite, the mineral component of bone and teeth. Despite the key role that these proteins play in the regulation of hard tissue growth in humans, the exact mechanism used by these proteins to recognize mineral surfaces is poorly understood. Interactions between mineral surfaces and proteins very likely involve specific contacts between the lattice and the protein side chains, so elucidation of the nature of interactions between protein side chains and their corresponding inorganic mineral surfaces will provide insight into the recognition and regulation of hard tissue growth. Isotropic chemical shifts, chemical shift anisotropies (CSAs), NMR line-width information, 13C rotating frame relaxation measurements, as well as direct detection of correlations between 13C spins on protein side chains and 31P spins in the crystal surface with REDOR NMR show that, in the peptide fragment derived from the N-terminal 15 amino acids of salivary statherin (i.e., SN-15), the side chain of the phenylalanine nearest the C-terminus of the peptide (F14) is dynamically constrained and oriented near the surface, whereas the side chain of the phenylalanine located nearest to the peptide’s N-terminus (F7) is more mobile and is oriented away from the hydroxyapatite surface. The relative dynamics and proximities of F7 and F14 to the surface together with prior data obtained for the side chain of SN-15’s unique lysine (i.e., K6) were used to construct a new picture for the structure of the surface-bound peptide and its orientation to the crystal surface.
2006. "Electrically Conductive Bacterial Nanowires Produced by Shewanella Oneidensis Strain MR-1 and Other Microorganisms ." Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363. Abstract Shewanella oneidensis MR-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. Mutants deficient in genes for c-type decaheme cytochromes MtrC and OmcA, and those that lacked a functional Type II secretion pathway displayed nanowires that were poorly conductive. These mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. Nanowires produced by the oxygenic phototrophic cyanobacterium Synechocystis PCC6803 and the thermophilic, fermentative bacterium Pelotomaculum thermopropionicum reveal that electrically conductive appendages are not exclusive to dissimilatory metal-reducing bacteria and may, in fact, represent a common bacterial strategy for efficient electron transfer and energy distribution.
2006. "Tribological performance of hybrid filtered arc-magnetron coatings - Part I: Coating deposition process and basic coating properties characterization." Surface & Coatings Technology 201(6):3732-3747. doi:10.1016/j.surfcoat.2006.09.007 Abstract Aircraft propulsion applications require low-friction and wear resistant surfaces that operate under high contact loads in severe environments. Recent research on supertough and low friction nanocomposite coatings produced with hybrid plasma deposition processes was demonstrated to have a high potential for such demanding applications. However, industrially scalable hybrid plasma technologies are needed for their commercial realization. The Large area Filtered Arc Deposition (LAFAD) process provides atomically smooth coatings at high deposition rates over large surface areas. The LAFAD technology allows functionally graded, multilayer, super-lattice and nanocomposite architectures of multi-elemental coatings via electro-magnetic mixing of two plasma flows composed of different metal ion vapors. Further advancement can be realized through a combinatorial process using a hybrid filtered arc-magnetron deposition system. In the present study, multilayer and nanostructured TiCrCN/TiCr +TiBC composite cermet coatings were deposited by the hybrid filtered arc-magnetron process. Filtered plasma streams from arc evaporated Ti and Cr targets, and two unbalanced magnetron sputtered B4C targets, were directed to the substrates in the presence of reactive gases. A multiphase nanocomposite coating architecture was designed to provide the optimal combination of corrosion and wear resistance of advanced steels (Pyrowear 675) used in aerospace bearing and gear applications. Coatings were characterized using SEM/EDS, XPS and RBS for morphology and chemistry, XRD and TEM for structural analyses, wafer curvature and nanoindentation for stress and mechanical properties, and Rockwell and scratch indentions for adhesion. Coating properties were evaluated for a variety of coating architectures. Thermodynamic modeling was used for estimation of phase composition of the top TiBC coating segment. Correlations between coating chemistry, structure and mechanical properties are discussed.
2006. "Vibrational Spectroscopy of Mass-Selected [UO₂(ligand)n]²⁺ Complexes in the Gas Phase: Comparison with Theory." Journal of the American Chemical Society 128(14):4802-4813. doi:10.1021/ja058106n Abstract The gas-phase infrared spectra of discrete uranyl ([UO₂]²⁺) complexes ligated with acetone and/or acetonitrile were used to evaluate systematic trends of ligation on the position of the O=U=O stretch, and to enable rigorous comparison with the results of computational studies. Ionic uranyl complexes isolated in a Fourier transform ion cyclotron resonance mass spectrometer were fragmented via infrared multiphoton dissociation using a free electron laser scanned over the mid-IR wavelengths. The asymmetric O=U=O stretching frequency was measured at 1017 cm⁻¹ for [UO₂(CH₃COCH₃)₂]²⁺ and was systematically red shifted to 1000 and 988 cm⁻¹ by the addition of a third and fourth acetone ligand, respectively, which was consistent with increased donation of electron density to the uranium center in complexes with higher coordination number. The values generated computationally using LDA, B3LYP, and ZORA-PW91 were in good agreement with experimental measurements. In contrast to the uranyl frequency shifts, the carbonyl frequencies of the acetone ligands were progressively blue shifted as the number of ligands increased from 2 to 4, and approached that of free acetone. This observation was consistent with the formation of weaker noncovalent bonds between uranium and the carbonyl oxygen as the extent of ligation increases. Similar trends were observed for [UO₂(CH₃CN)n]²⁺ complexes, although the magnitude of the red shift in the uranyl frequency upon addition of more acetonitrile ligands was smaller than for acetone, consistent with the more modest nucleophilic nature of acetonitrile. This conclusion was confirmed by the uranyl stretching frequencies measured for mixed acetone/acetonitrile complexes, which showed that substitution of one acetone for one acetonitrile produced a modest red shift of 3 to 6 cm⁻¹.
2006. "Thermal Oxidation of Aluminum Nitride Powder ." Journal of the American Ceramic Society 89(7):2167–2171. doi:10.1111/j.1551-2916.2006.01065.x Abstract The kinetics of the thermal oxidation of AlN powder in flowing oxygen over temperatures from 800 to 1150 °C and the morphology and crystallinity of the resultant oxide were determined. The oxidation of two types of AlN powder was investigated and compared. Complex difference in the oxidation behavior was observed, probably due to their different morphology, particle size, particle size distribution, and residual impurities. Amorphous alumina formed at relatively low oxidation temperatures (800-1000 °C), with a linear oxidation rate governed by interfacial reaction. Crystalline alumina formed at higher temperatures (>1000 °C), and the oxidation rate was parabolic which suggested an oxidant diffusion controlled process.
2006. "The Effect of Anteroapical Aneurysm Plication on End-Systolic Three-Dimensional Strain in the Sheep: A Magnetic Resonance Imaging Tagging Study." Journal of Thoracic and Cardiovascular Surgery 131(3):579-586. Abstract An abstract for this journal article is not available at this time.
2006. "Accurate Thermochemical Properties for Energetic Materials Applications. I. Heats ofFormation of Nitrogen-Containing Heterocycles and Energetic Precursor Molecules fromElectronic Structure Theory." Journal of Physical Chemistry A 110(42):11890-11897. doi:10.1021/jp0643698 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 heats of formation of 1H-imidazole, 1H-1,2,4-trizazole, 1H-tetrazole, CH3NO2, CH3N3, CH3NH2, CH2- CHNO2, HClO4, and phenol, as well as cations and anions derived from some of the molecules have been calculated using ab initio molecular orbital theory. These molecules are important as models for compounds used for energetic materials synthesis. The predicted heats of formation of the heterocycle-based compounds are in excellent agreement with available experimental values and those derived from proton affinities and deprotonation enthalpies to <1 kcal/mol. The predicted value for the tetrazolium cation differs substantially from the experimental value, likely due to uncertainty in the measurement. The heats of formation of the nitro and amino molecules, as well as phenol/phenolate, also are in good agreement with the experimental values (<1.5 kcal/mol). The heat of formation of CH3N3 is predicted to be 72.8 kcal/mol at 298 K with an estimated error bar of (1 kcal/mol on the basis of the agreement between the calculated and experimental values for ¢Hf(HN3). The heat of formation at 298 K of HClO4 is -0.4 kcal/mol, in very good agreement with the experimental value, as well as a W2 literature study. An extrapolation of the CCSD(T)/aug-cc-pV- (Q,5) energies was required to obtain this agreement. This result suggests that very large basis sets (gaugcc- pV5Z) may be needed to fully recover the valence correlation energy contribution in compounds containing elements with high formal oxidation states at the central atom. In addition tight d functions are needed for the geometry predictions. Douglas-Kroll-Hess (DKH) scalar relativistic corrections for HClO4 and ClO4 - at the MP2 level with correlation-consistent DKH basis sets were predicted to be large, likely due to the high formal oxidation state at the Cl.
2006. "Predicting the Energy of the Water Exchange Reaction and Free Energy of Solvation forthe Uranyl Ion in Aqueous Solution." Journal of Physical Chemistry A 110(28):8840-8856. doi:10.1021/jp061851h Abstract The structures and vibrational frequencies of UO₂(H₂O)₄ ²⁺ and UO₂(H₂O)₅ ²⁺ have been calculated using density functional theory and are in reasonable agreement with experiment. The energies of various reactions were calculated at the density functional theory (DFT) and MP2 levels; the latter provides the best results. Self-consistent reaction field calculations in the PCM and SCIPCM approximations predicted the free energy of the water exchange reaction, UO₂(H₂O)₄ ²⁺ + H₂O T UO₂(H₂O)₅ ²⁺. The calculated free energies of reaction are very sensitive to the choice of radii (O and H) and isodensity values in the PCM and SCIPCM models, respectively. Results consistent with the experimental HEXS value of -1.19 plus or minus 0.42 kcal/mol (within 1-3 kcal/mol) are obtained with small cavities. The structures and vibrational frequencies of the clusters with second solvation shell waters: UO₂2(H₂2O)₄(H₂2O)₈ ²⁺, UO₂(H₂O)₄(H₂O)sub10 ²⁺, UO₂(H₂O)₄(H₂O)sub11 ²⁺, UO₂(H₂O)₅- (H₂O)₇ ²⁺, and UO₂(H₂O)5(H₂O)sub10 ²⁺, were calculated and are in better agreement with experiment as compared to reactions involving only UO₂(H₂O)₄ ²⁺ and UO₂(H₂O)₅ ²⁺. The MP2 reaction energies for water exchange gave gas-phase results that agreed with experiment in the range -5.5 to +3.3 kcal/mol. The results were improved by inclusion of a standard PCM model with differences of -1.2 to +2.7 kcal/mol. Rearrangement reactions based on an intramolecular isomerization leading to a redistribution of water in the two shells provide good values in comparison to experiment with values of ∆Gexchange from -2.2 to -0.5 kcal/mol so the inclusion of a second hydration sphere accounts for most solvation effects. Calculation of the free energy of solvation of the uranyl cation yielded an upper bound to the solvation energy of -410 plus or minus 5 kcal/mol, consistent with the best experimental value of -421 plus or minus 15 kcal/mol.
2006. "Hydrogen Gets Onboard." Chemistry World (March 2006):, doi:www.rsc.org/chemistryworld/Issues/2006/March Abstract In this brief review we update progress in research efforts for on-board hydrogen storage for fuel cell powered vehicles. In addition to economic targets, the technological challenges are bounded by volumetric and gravimetric constraints. Specifically, an amoiunt of 4 kg of H2, required to propel a highly fuel efficient automobile for 500 kilometers, must fit into the space of a conventional gasoline tank. The volumetric constraints rule out compressed and liquefied H2 and teach us that hydrogen must be stored as a solid material, either by physi-sorption to high surface area materials or chemically bond (covalent or ionic) to light weight elements. Hydrogen stored on high surface area materials is weakly bound and general requires low temperatures to stabilize the hydrogen. On the other end, hydrogen covalently bound to light metals requires high temperatures to release the hydrogen. One interesting alterative is chemical hydrogen storage (CHS). CHS covers a broad range of materials but is defined as a process whereby the hydrogen is released by a chemical reaction. The reaction could be induced by hydrolysis, a reaction with water, or by thermolysis, heating to moderate temperatures to release hydrogen. The spent material can then be reprocessed or regenerated off-board. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.