Showing papers by "Pacific Northwest National Laboratory published in 2007"

Basis set exchange: a community database for computational sciences.

Abstract: Basis sets are some of the most important input data for computational models in the chemistry, materials, biology, and other science domains that utilize computational quantum mechanics methods. Providing a shared, Web-accessible environment where researchers can not only download basis sets in their required format but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a Web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.

Metal Chlorides in Ionic Liquid Solvents Convert Sugars to 5-Hydroxymethylfurfural

Abstract: Replacing petroleum feedstocks by biomass requires efficient methods to convert carbohydrates to a variety of chemical compounds. We report the catalytic conversion of sugars giving high yield to 5-hydroxymethylfurfural (HMF), a versatile intermediate. Metal halides in 1-alkyl-3-methylimidazolium chloride are catalysts, among which chromium (II) chloride is found to be uniquely effective, leading to the conversion of glucose to HMF with a yield near 70%. A wide range of metal halides is found to catalyze the conversion of fructose to HMF. Only a negligible amount of levulinic acid is formed in these reactions.

Historical Developments in Hydroprocessing Bio-oils

Abstract: This paper is a review of the developments in the field of catalytic hydroprocessing of biomass-derived liquefaction conversion products (bio-oil) over the past 25 years. Work has been underway, primarily in the U.S. and Europe, in catalytic hydrotreating and hydrocracking of bio-oil in both batch-fed and continuous-flow bench-scale reactor systems. A range of heterogeneous catalyst materials have been tested, including conventional sulfided catalysts developed for petroleum hydroprocessing and precious metal catalysts. The important processing differences have been identified, which required adjustments to conventional hydroprocessing as applied to petroleum feedstocks. This application of hydroprocessing is seen as an extension of petroleum processing and system requirements are not far outside the range of conventional hydroprocessing. The technology is still under development but can play a significant role in supplementing increasingly expensive petroleum.

Methanol steam reforming for hydrogen production.

Abstract: Review article covering developments in methanol steam reforming in the context of PEM fuel cell power systems. Subjects covered include methanol background, use, and production, comparison to other fuels, power system considerations, militrary requirements, competing technologies, catalyst development, and reactor and system development and demonstration.

The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

Abstract: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Removal of Heavy Metals from Aqueous Systems with Thiol Functionalized Superparamagnetic Nanoparticles

Abstract: We have shown that superparamagnetic iron oxide (Fe3O4) nanoparticles with a surface functionalization of dimercaptosuccinic acid (DMSA) are an effective sorbent material for toxic soft metals such as Hg, Ag, Pb, Cd, and Tl, which effectively bind to the DMSA ligands and for As, which binds to the iron oxide lattices. The nanoparticles are highly dispersible and stable in solutions, have a large surface area (114 m2/g), and have a high functional group content (1.8 mmol thiols/g). They are attracted to a magnetic field and can be separated from solution within a minute with a 1.2 T magnet. The chemical affinity, capacity, kinetics, and stability of the magnetic nanoparticles were compared to those of conventional resin based sorbents (GT-73), activated carbon, and nanoporous silica (SAMMS) of similar surface chemistries in river water, groundwater, seawater, and human blood and plasma. DMSA-Fe3O4 had a capacity of 227 mg of Hg/g, a 30-fold larger value than GT-73. The nanoparticles removed 99 wt % of 1 mg...

Mechanisms controlling soil carbon turnover and their potential application for enhancing carbon sequestration

Abstract: In addition to increasing plant C inputs, strategies for enhancing soil C sequestration include reducing C turnover and increasing its residence time in soils. Two major mechanisms, (bio)chemical alteration and physicochemical protection, stabilize soil organic C (SOC) and thereby control its turnover. With (bio)chemical alteration, SOC is transformed by biotic and abiotic processes to chemical forms that are more resistant to decomposition and, in some cases, more easily retained by sorption to soil solids. With physicochemical protection, biochemical attack of SOC is inhibited by organomineral interactions at molecular to millimeter scales. Stabilization of otherwise decomposable SOC can occur via sorption to mineral and organic soil surfaces, occlusion within aggregates, and deposition in pores or other locations inaccessible to decomposers and extracellular enzymes. Soil structure is a master integrating variable that both controls and indicates the SOC stabilization status of a soil. One potential option for reducing SOC turnover and enhancing sequestration, is to modify the soil physicochemical environment to favor the activities of fungi. Specific practices that could accomplish this include manipulating the quality of plant C inputs, planting perennial species, minimizing tillage and other disturbances, maintaining a near-neutral soil pH and adequate amounts of exchangeable base cations (particularly calcium), ensuring adequate drainage, and minimizing erosion. In some soils, amendment with micro- and mesoporous sorbents that have a high specific surface - such as fly ash or charcoal - can be beneficial.

Respiration of metal (hydr)oxides by shewanella and geobacter: a key role for multihaem c-type cytochromes

Abstract: Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram-negative bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c-type cytochromes (c-Cyts). In S. oneidensis MR-1, multihaem c-Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR-1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c-Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c-Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c-Cyts play critical roles in S. oneidensis MR-1- and G. sulfurreducens-mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope.

Current Production and Metal Oxide Reduction by Shewanella oneidensis MR-1 Wild Type and Mutants

Abstract: Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. S. oneidensis MR-1 can reduce Mn(IV) and Fe(III) oxides and can produce current in microbial fuel cells. The mechanisms that are employed by S. oneidensis MR-1 to execute these processes have not yet been fully elucidated. Several different S. oneidensis MR-1 deletion mutants were generated and tested for current production and metal oxide reduction. The results showed that a few key cytochromes play a role in all of the processes but that their degrees of participation in each process are very different. Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1.

Hierarchically Structured ZnO Film for Dye‐Sensitized Solar Cells with Enhanced Energy Conversion Efficiency

Abstract: The interest in dye-sensitized solar cells has increased due to reduced energy sources and higher energy production costs. For the most part, titania (TiO2) has been the material of choice for dye-sensitized solar cells and so far have shown to exhibit the highest overall light conversion efficiency ~ 11%.[1] However, zinc oxide (ZnO) has recently been explored as an alternative material in dye-sensitized solar cells with great potential.[2] The main reasons for this increase in research surrounding ZnO material include: 1) ZnO having a band gap similar to that for TiO2 at 3.2 eV,[3] and 2) ZnO having a much higher electron mobility ~ 115-155 cm2/Vs[4] than that for anatase titania (TiO2), which is reported to be ~ 10-5 cm2/Vs.[5] In addition, ZnO has a few advantages as the semiconductor electrode when compared to TiO2, including 1) simpler tailoring of the nanostructure as compared to TiO2, and 2) easier modification of the surface structure. These advantages[6] are thought to provide a promising means for improving the solar cell performance of the working electrode in dye-sensitized solar cells.

Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance

Abstract: In the hierarchy of cellular targets damaged by ionizing radiation (IR), classical models of radiation toxicity place DNA at the top. Yet, many prokaryotes are killed by doses of IR that cause little DNA damage. Here we have probed the nature of Mn-facilitated IR resistance in Deinococcus radiodurans, which together with other extremely IR-resistant bacteria have high intracellular Mn/Fe concentration ratios compared to IR-sensitive bacteria. For in vitro and in vivo irradiation, we demonstrate a mechanistic link between Mn(II) ions and protection of proteins from oxidative modifications that introduce carbonyl groups. Conditions that inhibited Mn accumulation or Mn redox cycling rendered D. radiodurans radiation sensitive and highly susceptible to protein oxidation. X-ray fluorescence microprobe analysis showed that Mn is globally distributed in D. radiodurans, but Fe is sequestered in a region between dividing cells. For a group of phylogenetically diverse IR-resistant and IR-sensitive wild-type bacteria, our findings support the idea that the degree of resistance is determined by the level of oxidative protein damage caused during irradiation. We present the case that protein, rather than DNA, is the principal target of the biological action of IR in sensitive bacteria, and extreme resistance in Mn-accumulating bacteria is based on protein protection.

Engineering void space in organic van der Waals crystals: calixarenes lead the way

Abstract: Seemingly non-porous organic solids have the ability for guest transport and have also been shown to absorb gases, including hydrogen, methane and acetylene, to varied extents. These materials also show potential for gas separation technology, display remarkable water transport through hydrophobic crystals, and clearly show that molecules within crystals are capable of cooperating with guests as they move through non-porous environments. This work is presented within a broader topic which also encompasses crystal engineering and (microporous) metal-organic frameworks (MOF's).

Electron transport via polaron hopping in bulk Ti O 2 : A density functional theory characterization

Abstract: In this work we describe our use of Marcus theory to model the electron transfer process in TiO2. Electron transport is described by a polaron model, whereby a photo-excited electron is localized at a Ti4+ site and hops to an adjacent Ti4+ site. We obtained the relevant parameters in Marcus theory (namely the activation energy ΔG*, the reorganization energy λ, and the electronic coupling matrix elements Vab) for selected crystallographic directions in rutile and anatase, using periodic DFT+U and Hartree-Fock cluster calculations. The DFT+U method was necessary to correct for the ubiquitous electron self-interaction problem? in DFT. Our results give non-adiabatic activation energies of similar magnitude in rutile and anatase, all near 0.3 eV. The electronic coupling matrix element, Vab, was determined to be largest for electron transfer parallel to the c direction in rutile, with a value of 0.20 eV, while the other directions investigated in both rutile and anatase gave Vab values near 0 eV. The results are indicative of adiabatic transfer (thermal hopping mechanism) in rutile and of diabatic transfer (tunneling mechanism) in anatase. This work was supported by the Office of Basic Energy Sciences of the Department of Energy, in part by the Chemical Sciences programmore » and in part by the Engineering and Geosciences Division. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

In situ solid state 11B MAS-NMR studies of the thermal decomposition of ammonia borane: mechanistic studies of the hydrogen release pathways from a solid state hydrogen storage material

Abstract: The mechanism of hydrogen release from solid state ammonia borane (AB) has been investigated via in situ solid state 11B and 11B{1H} MAS-NMR techniques in external fields of 7.1 T and 18.8 T at a decomposition temperature of 88 °C, well below the reported melting point. The decomposition of AB is well described by an induction, nucleation and growth mechanistic pathway. During the induction period, little hydrogen is released from AB; however, a new species identified as a mobile phase of AB is observed in the 11B NMR spectra. Subsequent to induction, at reaction times when hydrogen is initially being released, three additional species are observed: the diammoniate of diborane (DADB), [(NH3)2BH2]+[BH4]−, and two BH2N2 species believed to be the linear (NH3BH2NH2BH3) and cyclic dimer (NH2BH2)2 of aminoborane. At longer reaction times the sharper features are replaced by broad, structureless peaks of a complex polymeric aminoborane (PAB) containing both BH2N2 and BHN3 species. The following mechanistic model for the induction, nucleation and growth for AB decomposition leading to formation of hydrogen is proposed: (i) an induction period that yields a mobile phase of AB caused by disruption of the dihydrogen bonds; (ii) nucleation that yields reactive DADB from the mobile AB; and (iii) growth that includes a bimolecular reaction between DADB and AB to release the stored hydrogen.

Retrieving Liquid Wat0er Path and Precipitable Water Vapor From the Atmospheric Radiation Measurement (ARM) Microwave Radiometers

Abstract: Ground-based two-channel microwave radiometers (MWRs) have been used for over 15 years by the Atmospheric Radiation Measurement (ARM) program to provide observations of downwelling emitted radiance from which precipitable water vapor (PWV) and liquid water path (LWP) - two geophysical parameters critical for many areas of atmospheric research - are retrieved. An algorithm that incorporates output from two advanced retrieval techniques, namely, a physical-iterative approach and a computationally efficient statistical method, has been developed to retrieve these parameters. The forward model used in both methods is the monochromatic radiative transfer model MonoRTM. An important component of this MWR RETrieval (MWRRET) algorithm is the determination of small (< 1 K) offsets that are subtracted from the observed brightness temperatures before the retrievals are performed. Accounting for these offsets removes systematic biases from the observations and/or the model spectroscopy necessary for the retrieval, significantly reducing the systematic biases in the retrieved LWP. The MWRRET algorithm significantly provides more accurate retrievals than the original ARM statistical retrieval, which uses monthly retrieval coefficients. By combining the two retrieval methods with the application of brightness temperature offsets to reduce the spurious LWP bias in clear skies, the MWRRET algorithm significantly provides better retrievals of PWV and LWP from the ARM two-channel MWRs compared to the original ARM product.

The Mixed-Phase Arctic Cloud Experiment.

Abstract: The Mixed-Phase Arctic Cloud Experiment (M-PACE) was conducted September 27 through October 22, 2004 on the North Slope of Alaska. The primary objective was to collect a data set suitable to study interactions between microphysics, dynamics and radiative transfer in mixed-phase Arctic clouds. Observations taken during the 1997/1998 Surface Heat and Energy Budget of the Arctic (SHEBA) experiment revealed that Arctic clouds frequently consist of one (or more) liquid layers precipitating ice. M-PACE sought to investigate the physical processes of these clouds utilizing two aircraft (an in situ aircraft to characterize the microphysical properties of the clouds and a remote sensing aircraft to constraint the upwelling radiation) over the Department of Energy s Atmospheric Radiation Measurement (ARM) Climate Research Facility (ACRF) on the North Slope of Alaska. The measurements successfully documented the microphysical structure of Arctic mixed-phase clouds, with multiple in situ profiles collected in both single-layer and multi-layer clouds over two ground-based remote sensing sites. Liquid was found in clouds with temperatures down to -30 C, the coldest cloud top temperature below -40 C sampled by the aircraft. Remote sensing instruments suggest that ice was present in low concentrations, mostly concentrated in precipitation shafts, although there are indications of light ice precipitation present below the optically thick single-layer clouds. The prevalence of liquid down to these low temperatures could potentially be explained by the relatively low measured ice nuclei concentrations.

In vitro cell culture infectivity assay for human noroviruses.

Abstract: Human noroviruses cause severe, self-limiting gastroenteritis that typically lasts 24–48 hours. Because of the lack of suitable tissue culture or animal models, the true nature of norovirus pathogenesis remains unknown. We show that noroviruses can infect and replicate in a 3-dimensional (3-D), organoid model of human small intestinal epithelium. Cells grown on porous collage-coated beads under fluid shear conditions in rotating wall vessel bioreactors differentiate into 3-D architectures resembling both the morphologic and physiologic function of in vivo tissues. Microscopy, PCR, and fluorescent in situ hybridization provided evidence of norovirus infection. Cytopathic effect and norovirus RNA were detected at each of the 5 cell passages for genogroup I and II viruses. Our results demonstrate that the highly differentiated 3-D cell culture model can support the natural growth of human noroviruses, whereas previous attempts that used differentiated monolayer cultures failed.

AC Versus DC Distribution SystemsDid We Get it Right

Abstract: We presently enjoy a predominantly AC electrical distribution system, the engineering basis for which was designed over 100 years ago. While AC distribution systems have served us well, we should periodically pause to assess what opportunities we have accepted or been denied by the overwhelming predominance of AC electrical power distribution systems. What opportunities could be obtained by engineering DC distribution into at least portions of our present system? What advantages of the present AC distribution system should be recognized and protected? This paper will focus on distribution within premise and low-voltage distribution systems. Specifically, we will address the conversion efficiency costs of adopting various premise AC and DC distribution system topologies. According to a simple predictive model formulated in this paper, premise residential DC distribution will incur unfavorable total conversion efficiency compared with existing AC premise distribution. However, if a residence is supplied by a fuel cell or another DC generator, the total conversion efficiency within a residential DC distribution system could be similar to, or even better than, that for AC distribution.

Structural criteria for the design of anion receptors: the interaction of halides with electron-deficient arenes.

Abstract: This paper refines the nature of the interactions between electron-deficient arenes and halide anions. Conclusions are based on (i) new crystal structures containing alkali halide salts with 1,2,4,5-tetracyanobenzene (TCB) and 18-crown-6, (ii) evaluation of crystal structures found in the Cambridge Structural Database, and (iii) MP2/aug-cc-pVDZ calculations of F-, Cl-, and Br- complexes with TCB, 1,3,5-tricyanobenzene, triazine, and hexafluorobenzene. When the halide lies above the plane of the π system, the results establish that three distinctly different types of complexes are possible: strongly covalent σ complexes, weakly covalent donor−π-acceptor complexes, and noncovalent anion−π complexes. When aryl C−H groups are present, a fourth type of interaction leads to C−H · · · X- hydrogen bonding. Characterization of the different geometries encountered with the four possible binding motifs provides criteria needed to design host architectures containing electron-deficient arenes.

Nature of hydrogen interactions with Ni(II) complexes containing cyclic phosphine ligands with pendant nitrogen bases

Abstract: Studies of the role of proton relays in molecular catalysts for the electrocatalytic production and oxidation of H2 have been carried out. The electrochemical production of hydrogen from protonated DMF solutions catalyzed by [Ni(P2PhN2Ph)2(CH3CN)](BF4)2, 3a (where P2PhN2Ph is 1,3,5,7-tetraphenyl-1,5-diaza-3,7-diphosphacyclooctane), permits a limiting value of the H2 production rate to be determined. The turnover frequency of 350 s−1 establishes that the rate of H2 production for the mononuclear nickel catalyst 3a is comparable to those observed for Ni-Fe hydrogenase enzymes. In the electrochemical oxidation of hydrogen catalyzed by [Ni(P2CyN2Bz)2](BF4)2, 3b (where Cy is cyclohexyl and Bz is benzyl), the initial step is the reversible addition of hydrogen to 3b (Keq = 190 atm−1 at 25°C). The hydrogen addition product exists as three nearly isoenergetic isomers 4A–4C, which have been identified by a combination of one- and two-dimensional 1H, 31P, and 15N NMR spectroscopies as Ni(0) complexes with a protonated amine in each cyclic ligand. The nature of the isomers, together with calculations, suggests a mode of hydrogen activation that involves a symmetrical interaction of a nickel dihydrogen ligand with two amine bases in the diphosphine ligands. Single deprotonation of 4 by an external base results in a rearrangement to [HNi(P2CyN2Bz)2](BF4), 5, and this reaction is reversed by the addition of a proton to the nickel hydride complex. The small energy differences associated with significantly different distributions in electron density and protons within these molecules may contribute to their high catalytic activity.

Variational Transition State Theory with Multidimensional Tunneling

Abstract: This review describes the application of variational transition state theory (VTST) to the calculation of chemical reaction rates In 1985 two of us, together with Alan D Isaacson, wrote a book chapter on this subject entitled “Generalized Transition State Theory” for the multi-volume series entitled Theory of Chemical Reaction Dynamics1 Since that time, variational transition state theory has undergone important improvements due mainly to the ability of this theory to adapt to more challenging problems For instance, the 1985 chapter mainly describes the application of VTST to bimolecular reactions involving 3–6 atoms, which were the state-of-the-art at that moment The study of those reactions by VTST dynamics depended on the construction of an analytical potential energy surface (PES) Nowadays, thanks to the development of more efficient algorithms and more powerful computers, the situation is completely different, and most rate calculations are based on “on the fly” electronic structure calculations, which together with hybrid approaches, like combined quantum mechanical molecular mechanical methods (QM/MM), allow researchers to apply VTST to systems with hundreds or even tens of thousands of atoms Three other major advances since 1985 are that transition state dividing surfaces can now be defined much more realistically, more accurate methodsmore » have been developed to include multidimensional quantum mechanical tunneling into VTST, and the theory has also been extended to reactions in condensed phases« less