Environmental Molecular science Laboratory

Richland, WA, United States

Environmental Molecular science Laboratory

Richland, WA, United States
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Wang C.-M.,Environmental Molecular science Laboratory | Li X.,Fundamental and Computational Science Directorate | Wang Z.,Fundamental and Computational Science Directorate | Xu W.,Pacific Northwest National Laboratory | And 10 more authors.
Nano Letters | Year: 2012

It is well-known that upon lithiation, both crystalline and amorphous Si transform to an armorphous Li xSi phase, which subsequently crystallizes to a (Li, Si) crystalline compound, either Li 15Si 4 or Li 22Si 5. Presently, the detailed atomistic mechanism of this phase transformation and the degradation process in nanostructured Si are not fully understood. Here, we report the phase transformation characteristic and microstructural evolution of a specially designed amorphous silicon (a-Si) coated carbon nanofiber (CNF) composite during the charge/discharge process using in situ transmission electron microscopy and density function theory molecular dynamic calculation. We found the crystallization of Li 15Si 4 from amorphous Li xSi is a spontaneous, congruent phase transition process without phase separation or large-scale atomic motion, which is drastically different from what is expected from a classic nucleation and growth process. The a-Si layer is strongly bonded to the CNF and no spallation or cracking is observed during the early stages of cyclic charge/discharge. Reversible volume expansion/contraction upon charge/discharge is fully accommodated along the radial direction. However, with progressive cycling, damage in the form of surface roughness was gradually accumulated on the coating layer, which is believed to be the mechanism for the eventual capacity fade of the composite anode during long-term charge/discharge cycling. © 2012 American Chemical Society.


Heiden Z.M.,Pacific Northwest National Laboratory | Chen S.,Pacific Northwest National Laboratory | Labios L.A.,Pacific Northwest National Laboratory | Bullock R.M.,Pacific Northwest National Laboratory | And 3 more authors.
Organometallics | Year: 2014

Protonation of an iron C-H activated complex containing pendant amines in the presence of N2 generated a cis-(H)FeII-N2 complex. Addition of acid protonates the pendant amines. Reduction of the protonated complex results in N2 loss and H2 formation, followed by N2 binding. The origin of H2 formation in this Fe system is compared to proposed mechanisms for H2 loss and N 2 coordination in the E4 state of nitrogenase. © 2014 American Chemical Society.


Miliordos E.,Pacific Northwest National Laboratory | Apra E.,Environmental Molecular science Laboratory | Xantheas S.S.,Pacific Northwest National Laboratory
Journal of Chemical Physics | Year: 2013

We report the first optimum geometries and harmonic vibrational frequencies for the ring pentamer and several water hexamer (prism, cage, cyclic and two book) at the coupled-cluster including single, double, and full perturbative triple excitations (CCSD(T))/aug-cc-pVDZ level of theory. All five examined hexamer isomer minima previously reported by Møller-Plesset perturbation theory (MP2) are also minima on the CCSD(T) potential energy surface (PES). In addition, all CCSD(T) minimum energy structures for the n = 2-6 cluster isomers are quite close to the ones previously obtained by MP2 on the respective PESs, as confirmed by a modified Procrustes analysis that quantifies the difference between any two cluster geometries. The CCSD(T) results confirm the cooperative effect of the homodromic ring networks (systematic contraction of the nearest-neighbor (nn) intermolecular separations with cluster size) previously reported by MP2, albeit with O-O distances shorter by ∼0.02 Å, indicating that MP2 overcorrects this effect. The harmonic frequencies at the minimum geometries were obtained by the double differentiation of the CCSD(T) energy using an efficient scheme based on internal coordinates that reduces the number of required single point energy evaluations by ∼15% when compared to the corresponding double differentiation using Cartesian coordinates. Negligible differences between MP2 and CCSD(T) frequencies are found for the librational modes, while uniform increases of ∼15 and ∼25 cm-1 are observed for the bending and "free" OH harmonic frequencies. The largest differences between CCSD(T) and MP2 are observed for the harmonic hydrogen bonded frequencies, for which the former produces larger absolute values than the latter. Their CCSD(T) redshifts from the monomer values (δω) are smaller than the MP2 ones, due to the fact that CCSD(T) produces shorter elongations (δR) of the respective hydrogen bonded OH lengths from the monomer value with respect to MP2. Both the MP2 and CCSD(T) results for the hydrogen bonded frequencies were found to closely follow the relation -δω = s · δR, with a rate of s = 20.2 cm -1/0.001 Å for hydrogen bonded frequencies with IR intensities >400 km/mol. The CCSD(T) harmonic frequencies, when corrected using the MP2 anharmonicities obtained from second order vibrational perturbation theory, produce anharmonic CCSD(T) estimates that are within <60 cm-1from the measured infrared (IR) active bands of the n = 2-6 clusters. Furthermore, the CCSD(T) harmonic redshifts (with respect to the monomer) trace the measured ones quite accurately. The energetic order between the various hexamer isomers on the PES (prism has the lowest energy) previously reported at MP2 was found to be preserved at the CCSD(T) level, whereas the inclusion of anharmonic corrections further stabilizes the cage among the hexamer isomers. © 2013 AIP Publishing LLC.


Laskin A.,Environmental Molecular science Laboratory | Laskin J.,Pacific Northwest National Laboratory | Nizkorodov S.A.,University of California at Irvine
Chemical Reviews | Year: 2015

The chemistry of atmospheric brown carbon (BrC) is reviewed. BrC is now recognized as an important component in the atmosphere that affects climate forcing through a combination of direct effects on the transmission of solar and terrestrial radiation and indirect effects resulting from changes in cloud formation and microphysics. In addition, long-range transport and deposition of BrC most likely play a role in carbon and nitrogen cycling between atmosphere, land, and water and contribute to the formation of colored dissolved organic matter (CDOM). The existing evidence suggests that even a very small weight fraction of strongly absorbing BrC chromophores may have a distinct effect on organic aerosols (OA) optical properties. Because of the low concentrations of light-absorbing molecules in complex organic mixtures composing both laboratory-generated and ambient OA, identification of BrC chromophores is a very challenging task. Despite the analytical difficulties, several classes of compounds have been identified as potential contributors to light absorption by BrC. These include nitroaromatic compounds, such as nitrophenols, imidazole-based and other N-heterocyclic compounds, and quinines. The identification and structural characterization of BrC chromophores clearly require highly sensitive molecular characterization approaches capable of detecting both strongly and weakly absorbing species.


Devaraj A.,Environmental Molecular science Laboratory | Colby R.,Environmental Molecular science Laboratory | Hess W.P.,Pacific Northwest National Laboratory | Perea D.E.,Environmental Molecular science Laboratory | Thevuthasan S.,Environmental Molecular science Laboratory
Journal of Physical Chemistry Letters | Year: 2013

The addition of pulsed lasers to atom probe tomography (APT) extends its high spatial and mass resolution capability to nonconducting materials, such as oxides. For a prototypical metal oxide, MgO, the measured stoichiometry depends strongly on the laser pulse energy and applied voltage. Very low laser energies (0.02 pJ) and high electric fields yield optimal stoichiometric accuracy. Correlated APT and aberration-corrected transmission electron microscopy (TEM) are used to establish the high density of corner and terrace sites on MgO sample surfaces before and after APT. For MgO, long-lifetime photoexcited holes localized at oxygen corner sites can assist in the creation of oxygen neutrals that may spontaneously desorb either as atomic O or as molecular O2. The observed trends are best explained by the relative field-dependent ionization of photodesorbed O or O2 neutrals. These results emphasize the importance of considering electronic excitations in APT analysis of oxide materials. © 2013 American Chemical Society.


Bagwell C.E.,Savannah River National Laboratory | Hixson K.K.,Environmental Molecular science Laboratory | Milliken C.E.,Savannah River National Laboratory | Lopez-Ferrer D.,Pacific Northwest National Laboratory | Weitz K.K.,Pacific Northwest National Laboratory
PLoS ONE | Year: 2010

Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0-1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R2 = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration. © 2010 Bagwell et al.


Abdul Halim M.F.,University of Pennsylvania | Pfeiffer F.,Max Planck Institute of Biochemistry | Zou J.,University of Pennsylvania | Frisch A.,University of Pennsylvania | And 7 more authors.
Molecular Microbiology | Year: 2013

Cell surfaces are decorated by a variety of proteins that facilitate interactions with their environments and support cell stability. These secreted proteins are anchored to the cell by mechanisms that are diverse, and, in archaea, poorly understood. Recently published in silico data suggest that in some species a subset of secreted euryarchaeal proteins, which includes the S-layer glycoprotein, is processed and covalently linked to the cell membrane by enzymes referred to as archaeosortases. In silico work led to the proposal that an independent, sortase-like system for proteolysis-coupled, carboxy-terminal lipid modification exists in bacteria (exosortase) and archaea (archaeosortase). Here, we provide the first in vivo characterization of an archaeosortase in the haloarchaeal model organism Haloferax volcanii. Deletion of the artA gene (HVO_0915) resulted in multiple biological phenotypes: (a) poor growth, especially under low-salt conditions, (b) alterations in cell shape and the S-layer, (c) impaired motility, suppressors of which still exhibit poor growth, and (d) impaired conjugation. We studied one of the ArtA substrates, the S-layer glycoprotein, using detailed proteomic analysis. While the carboxy-terminal region of S-layer glycoproteins, consisting of a putative threonine-rich O-glycosylated region followed by a hydrophobic transmembrane helix, has been notoriously resistant to any proteomic peptide identification, we were able to identify two overlapping peptides from the transmembrane domain present in the ΔartA strain but not in the wild-type strain. This clearly shows that ArtA is involved in carboxy-terminal post-translational processing of the S-layer glycoprotein. As it is known from previous studies that a lipid is covalently attached to the carboxy-terminal region of the S-layer glycoprotein, our data strongly support the conclusion that archaeosortase functions analogously to sortase, mediating proteolysis-coupled, covalent cell surface attachment. © 2013 John Wiley & Sons Ltd.


Bateman A.P.,University of California at Irvine | Nizkorodov S.A.,University of California at Irvine | Laskin J.,Environmental Molecular science Laboratory | Laskin A.,Pacific Northwest National Laboratory
Analytical Chemistry | Year: 2010

This work demonstrates the utility of a particle-into-liquid sampler (PILS), a technique traditionally used for identification of inorganic ions present in ambient or laboratory aerosols, for the analysis of water-soluble organic aerosol (OA) using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). Secondary organic aerosol (SOA) was produced from 0.5 ppm mixing ratios of limonene and ozone in a 5 m 3 Teflon chamber. SOA was collected simultaneously using a traditional filter sampler and a PILS. The filter samples were later extracted with either water or acetonitrile, while the aqueous PILS samples were analyzed directly. In terms of peak abundances, types of detectable compounds, average O/C ratios, and organic mass to organic carbon ratios, the resulting high-resolution mass spectra were essentially identical for the PILS and filter based samples. SOA compounds extracted from both filter/acetonitrile extraction and PILS/water extraction accounted for >95% of the total ion current in the ESI mass spectra. This similarity was attributed to high solubility of limonene SOA in water. In contrast, significant differences in detected ions and peak abundances were observed for pine needle biomass burning organic aerosol (BBOA) collected with PILS and filter sampling. The water-soluble fraction of BBOA is considerably smaller than for SOA, and a number of unique peaks were detectable only by the filter/acetonitrile method. The combination of PILS collection with HR-ESI-MS analysis offers a new approach for molecular analysis of the water-soluble organic fraction in biogenic SOA, aged photochemical smog, and BBOA. © 2010 American Chemical Society.


Atta-Fynn R.,Environmental Molecular science Laboratory | Johnson D.F.,Environmental Molecular science Laboratory | Bylaska E.J.,Environmental Molecular science Laboratory | Ilton E.S.,Pacific Northwest National Laboratory | And 2 more authors.
Inorganic Chemistry | Year: 2012

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U 4+) and uranyl(V) (UO 2 +) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO 2 2+) are also probed. The first shell of U 4+ is coordinated by 8-9 water ligands, with an average U-O distance of 2.42 Å. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 Å, respectively. The simulated EXAFS of U 4+ matches well with recent experimental data. The first shell of UO 2 + is coordinated by five water ligands in the equatorial plane, with the average U-O ax and U-O distances being 1.85 Å and 2.54 Å, respectively. Overall, the hydration shell structure of UO 2 + closely matches that of UO 2 2+, except for small expansions in the average U-O ax and U-O distances. Each ion strongly polarizes their respective first-shell water ligands. The computed acidity constants (pK a) of U 4+ and UO 2 2+ are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24, respectively. The predicted pK a value of UO 2 + is 8.5. © 2012 American Chemical Society.


Brechenmacher L.,University of Missouri | Nguyen T.H.N.,University of Missouri | Hixson K.,Environmental Molecular science Laboratory | Libault M.,University of Missouri | And 3 more authors.
Proteomics | Year: 2012

Root hairs (RH) are a terminally differentiated single cell type, mainly involved in water and nutrient uptake from the soil. The soybean RH cell represents an excellent model for the study of single cell systems biology. In this study, we identified 5702 proteins, with at least two peptides, from soybean RH using an accurate mass and time tag approach, establishing a comprehensive proteome reference map of this single cell type. We also showed that trypsin is the most appropriate enzyme for soybean proteomic studies by performing an in silico digestion of the soybean proteome using different proteases. Although the majority of proteins identified in this study are involved in basal metabolism, the function of others are more related to RH formation/function and include proteins involved in nutrient uptake (transporters) or vesicular trafficking (cytoskeleton and ras-associated binding proteins). Interestingly, some of these proteins appear to be specifically detected in RH and constitute promising candidates for further studies to elucidate unique features of this single-cell model. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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