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.
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.
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.
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.