Showing papers by "Environmental Molecular Sciences Laboratory published in 2010"
TL;DR: An overview of NWChem is provided focusing primarily on the core theoretical modules provided by the code and their parallel performance, as well as Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures.
4,666 citations
TL;DR: Because lithiation-induced volume expansion, plasticity, and pulverization of electrode materials are the major mechanical effects that plague the performance and lifetime of high-capacity anodes in lithium-ion batteries, these observations provide important mechanistic insight for the design of advanced batteries.
Abstract: We report the creation of a nanoscale electrochemical device inside a transmission electron microscope--consisting of a single tin dioxide (SnO(2)) nanowire anode, an ionic liquid electrolyte, and a bulk lithium cobalt dioxide (LiCoO(2)) cathode--and the in situ observation of the lithiation of the SnO(2) nanowire during electrochemical charging. Upon charging, a reaction front propagated progressively along the nanowire, causing the nanowire to swell, elongate, and spiral. The reaction front is a "Medusa zone" containing a high density of mobile dislocations, which are continuously nucleated and absorbed at the moving front. This dislocation cloud indicates large in-plane misfit stresses and is a structural precursor to electrochemically driven solid-state amorphization. Because lithiation-induced volume expansion, plasticity, and pulverization of electrode materials are the major mechanical effects that plague the performance and lifetime of high-capacity anodes in lithium-ion batteries, our observations provide important mechanistic insight for the design of advanced batteries.
1,398 citations
TL;DR: In this article, the authors reported that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data, and when E. coli adapts to growth rate selective pressure, the evolved strains upregulated genes within the optimal growth predictions, and downregulated genes outside of the optimal solutions.
Abstract: After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild-type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild-type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM-computed optimal growth states.
636 citations
TL;DR: In this paper, the authors performed proteomic and lipidomic profiling over a time course of acute hepatitis C virus (HCV) infection in cultured Huh-7.5 cells to gain new insights into the intracellular processes influenced by this virus.
Abstract: Proteomic and lipidomic profiling was performed over a time course of acute hepatitis C virus (HCV) infection in cultured Huh-7.5 cells to gain new insights into the intracellular processes influenced by this virus. Our proteomic data suggest that HCV induces early perturbations in glycolysis, the pentose phosphate pathway, and the citric acid cycle, which favor host biosynthetic activities supporting viral replication and propagation. This is followed by a compensatory shift in metabolism aimed at maintaining energy homeostasis and cell viability during elevated viral replication and increasing cellular stress. Complementary lipidomic analyses identified numerous temporal perturbations in select lipid species (e.g. phospholipids and sphingomyelins) predicted to play important roles in viral replication and downstream assembly and secretion events. The elevation of lipotoxic ceramide species suggests a potential link between HCV-associated biochemical alterations and the direct cytopathic effect observed in this in vitro system. Using innovative computational modeling approaches, we further identified mitochondrial fatty acid oxidation enzymes, which are comparably regulated during in vitro infection and in patients with histological evidence of fibrosis, as possible targets through which HCV regulates temporal alterations in cellular metabolic homeostasis.
379 citations
TL;DR: EPS secreted by suspended cultures of microorganisms from an activated sludge plant in the presence of glucose were characterized in detail using colorimetry, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) Spectroscopy.
379 citations
TL;DR: The most stable surface of rutile TiO 2 (1/1/0) has become a prototypical model for fundamental studies of catalytic and photocatalytic reactions as mentioned in this paper.
282 citations
TL;DR: Nanosized zeolitic imidazolate frameworks [nZIF-8] with excellent chemical and thermal stability have been synthesized at room temperature by simple mixing of 2-methylimidazole and zinc nitrate hexahydrate in methanol/1% high molecular weight poly(diallyldimethylammonium chloride) chloride solution.
229 citations
TL;DR: This work demonstrates plasmonic nanofocusing into a localized excitation of approximately 20 nm in size and investigates its near- and far-field behavior and demonstrates the use of these tips as a source for nearly background-free scattering-type scanning near-field optical microscopy (s-SNOM).
Abstract: Focusing light to subwavelength dimensions has been a long-standing desire in optics but has remained challenging, even with new strategies based on near-field effects, polaritons, and metamaterials. The adiabatic propagation of surface plasmon polaritons (SPP) on a conical taper as proposed theoretically has recently emerged as particularly promising to obtain a nanoconfined light source at the tip. Employing grating-coupling of SPPs onto gold tips, we demonstrate plasmonic nanofocusing into a localized excitation of approximately 20 nm in size and investigate its near- and far-field behavior. For cone angles of approximately 10-20 degrees , the breakdown of the adiabatic propagation conditions is found to be localized at or near the apex region with approximately 10 nm radius. Despite an asymmetric side-on SPP excitation, the apex far-field emission with axial polarization characteristics representing a radially symmetric SPP mode in the nanofocus confirms that the conical tip acts as an effective mode filter with only the fundamental radially symmetric TM mode (m = 0) propagating to the apex. We demonstrate the use of these tips as a source for nearly background-free scattering-type scanning near-field optical microscopy (s-SNOM).
188 citations
TL;DR: The chemical composition of secondary organic aerosol (SOA) generated from the ozonolysis of isoprene (C5H8) in the presence of an OH scavenger was examined using high-resolution electrospray ionization mass spectrometry (ESI-MS) as discussed by the authors.
177 citations
TL;DR: In this paper, the authors examined the types of information that XPS can provide about a variety of nanostructured materials, including elemental distributions, layer or coating structure and thicknesses, surface functionality, and even particles sizes on the 1-20nm scale.
176 citations
TL;DR: The preliminary results from a small cohort of subjects in this study and healthy controls show a unique time-dependent gene expression pattern clearly demonstrating the ability of this tool to discriminate temporal transcriptional events of neutrophils within a clinical setting.
Abstract: Neutrophils have key roles in modulating the immune response. We present a robust methodology for rapidly isolating neutrophils directly from whole blood with 'on-chip' processing for mRNA and protein isolation for genomics and proteomics. We validate this device with an ex vivo stimulation experiment and by comparison with standard bulk isolation methodologies. Last, we implement this tool as part of a near-patient blood processing system within a multi-center clinical study of the immune response to severe trauma and burn injury. The preliminary results from a small cohort of subjects in our study and healthy controls show a unique time-dependent gene expression pattern clearly demonstrating the ability of this tool to discriminate temporal transcriptional events of neutrophils within a clinical setting.
TL;DR: This study presents the first application of desorption electrospray ionization combined with high-resolution mass spectrometry (DESI-MS) for detailed chemical characterization and studies of chemical aging of organic aerosol (OA) samples collected on Teflon substrates.
Abstract: Characterization of the chemical composition and chemical transformations of secondary organic aerosol (SOA) is both a major challenge and the area of greatest uncertainty in current aerosol research. This study presents the first application of desorption electrospray ionization combined with high-resolution mass spectrometry (DESI-MS) for detailed chemical characterization and studies of chemical aging of organic aerosol (OA) samples collected on Teflon substrates. DESI-MS offers unique advantages both for detailed characterization of chemically labile components in OA that cannot be detected using traditional electrospray ionization mass spectrometry (ESI-MS) and for studying chemical aging of OA. DESI-MS enables rapid characterization of OA samples collected on substrates by eliminating the sample preparation stage. In addition, it enables detection and structural characterization of chemically labile molecules in OA samples by minimizing the residence time of analyte in the solvent. In this study, DE...
TL;DR: The LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides from the high concentration mouse peptide matrix components, reducing signal interference and background, and allowing species to be resolved that would otherwise be obscured by other components.
Abstract: A high-throughput approach and platform using 15 min reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking 20 reference peptides at varying concentrations from 1 ng/mL to 10 μg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected 13 out of the 20 spiked peptides that had concentrations ≥100 ng/mL. In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for 19 of the 20 peptides with all spiking levels present. The greater dynamic range of the LC-IMS-TOF MS system could be attributed to two factors. First, the LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides fr...
TL;DR: Proteomic analysis of urine from patients with prostate cancer identified CD90; conversely, CD90 was not detected in the urine of post-prostatectomy patients, and this urinary CD90 protein was a variant CD90protein not known to be expressed by such cells as lymphocytes that express CD90.
TL;DR: This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen.
TL;DR: An automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edgeX-ray fine structure spectroscopy (STXM/NEXAFS) and the application of the automated mapping algorithms for data analysis and the statistical classification of particles.
Abstract: We have developed an automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure spectroscopy (STXM/NEXAFS). This method is applied to complex internally mixed submicrometer particles containing organic and inorganic material. Several algorithms were developed to exploit NEXAFS spectral features in the energy range from 278 to 320 eV for quantitative mapping of the spatial distribution of elemental carbon, organic carbon, potassium, and noncarbonaceous elements in particles of mixed composition. This energy range encompasses the carbon K-edge and potassium L2 and L3 edges. STXM/NEXAFS maps of different chemical components were complemented with a subsequent analysis using elemental maps obtained by scanning electron microscopy coupled with energy dispersive X-ray analysis (SEM/EDX). We demonstrate the application of the automated mapping algorithms for data analysis and the statistical classification of particles.
TL;DR: It is shown that high-resolution differential ion mobility spectrometry (FAIMS) employing helium-rich gases can readily separate phosphopeptides with variant modification sites, and anticipate FAIMS capabilities for such separations to extend to other PTMs.
Abstract: Many proteins and proteolytic peptides incorporate the same post-translational modification (PTM) at different sites, creating multiple localization variants with different functions or activities that may coexist in cells. Current analytical methods based on liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS) are challenged by such isomers that often coelute in LC and/or produce nonunique fragment ions. The application of ion mobility spectrometry (IMS) was explored, but success has been limited by insufficient resolution. We show that high-resolution differential ion mobility spectrometry (FAIMS) employing helium-rich gases can readily separate phosphopeptides with variant modification sites. Use of He/N(2) mixtures containing up to 74% He has allowed separating to >95% three monophosphorylated peptides of identical sequence. Similar separation was achieved at 50% He, using an elevated electric field. Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate FAIMS capabilities for such separations to extend to other PTMs.
TL;DR: The optical analogue of the radio frequency vector network analyzer implemented in interferometric homodyne scattering-type scanning near-field optical microscopy for obtaining E, H, and J(r) is demonstrated.
Abstract: In addition to the electric field $\mathbit{E}(\mathbit{r})$, the associated magnetic field $\mathbit{H}(\mathbit{r})$ and current density $\mathbit{J}(\mathbit{r})$ characterize any electromagnetic device, providing insight into antenna coupling and mutual impedance. We demonstrate the optical analogue of the radio frequency vector network analyzer implemented in interferometric homodyne scattering-type scanning near-field optical microscopy for obtaining $\mathbit{E}(\mathbit{r})$, $\mathbit{H}(\mathbit{r})$, and $\mathbit{J}(\mathbit{r})$. The approach is generally applicable and demonstrated for the case of a linear coupled-dipole antenna in the midinfrared spectral region. The determination of the underlying 3D vector electric near-field distribution $\mathbit{E}(\mathbit{r})$ with nanometer spatial resolution and full phase and amplitude information is enabled by the design of probe tips with selectivity with respect to ${E}_{\ensuremath{\parallel}}$ and ${E}_{\ensuremath{\perp}}$ fabricated by focused ion-beam milling and nano-chemical-vapor-deposition methods.
TL;DR: In this article, the physical and chemical transformations of particles aged in the outflow from Mexico City were investigated for the transport event of 22 March 2006 using a combination of complementary microscopy and micro-spectroscopy techniques.
Abstract: . This study was part of the Megacities Initiative: Local and Global Research Observations (MILAGRO) field campaign conducted in Mexico City metropolitan area during spring 2006. The physical and chemical transformations of particles aged in the outflow from Mexico City were investigated for the transport event of 22 March 2006. A detailed chemical analysis of individual particles was performed using a combination of complementary microscopy and micro-spectroscopy techniques. The applied techniques included scanning transmission X-ray microscopy (STXM) coupled with near edge X-ray absorption fine structure spectroscopy (NEXAFS) and computer controlled scanning electron microscopy with an energy dispersive X-ray analyzer (CCSEM/EDX). As the aerosol plume evolves from the city center, the organic mass per particle increases and the fraction of carbon-carbon double bonds (associated with elemental carbon) decreases. Organic functional groups enhanced with particle age include: carboxylic acids, alkyl groups, and oxygen bonded alkyl groups. At the city center (T0) the most prevalent aerosol type contained inorganic species (composed of sulfur, nitrogen, oxygen, and potassium) coated with organic material. At the T1 and T2 sites, located northeast of T0 (~29 km and ~65 km, respectively), the fraction of homogenously mixed organic particles increased in both size and number. These observations illustrate the evolution of the physical mixing state and organic bonding in individual particles in a photochemically active environment.
TL;DR: In this article, the onset of heterogeneous ice nucleation was observed as a function of particle temperature (Tp), relative humidity (RH), nucleation mode, and particle chemical composition which is influenced by photochemical atmospheric aging.
Abstract: This study reports on heterogeneous ice nucleation activity of predominantly organic (or coated with organic material) anthropogenic particles sampled within and around the polluted environment of Mexico City. The onset of heterogeneous ice nucleation was observed as a function of particle temperature (Tp), relative humidity (RH), nucleation mode, and particle chemical composition which is influenced by photochemical atmospheric aging. Particle analyses included computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS). In contrast to most laboratory studies employing proxies of organic aerosol, we show that anthropogenic organic particles collected in Mexico City can potentially induce ice nucleation at experimental conditions relevant to cirrus formation. The results suggest a new precedent for the potential impact of organic particles on ice cloud formation and climate.
TL;DR: In this article, the formation and transformation of water-induced cobalt oxide species during the reaction were influenced by the pre-reduced 10% Co/CeO2-ZrO2 catalyst.
TL;DR: Core-shell diamond particles for solid-phase extraction (SPE) and high-performance liquid chromatography (HPLC) made by layer-by-layer (LbL) deposition have much higher surface areas and analyte loading capacities in SPE than nonporous solid diamond particles.
Abstract: We report the formation of core−shell diamond particles for solid-phase extraction (SPE) and high-performance liquid chromatography (HPLC) made by layer-by-layer (LbL) deposition. Their synthesis begins with the amine functionalization of microdiamond by its immersion in an aqueous solution of a primary amine-containing polymer (polyallylamine (PAAm)). The amine-terminated microdiamond is then immersed in an aqueous suspension of nanodiamond, which leads to adsorption of the nanodiamond. Alternating (self-limiting) immersions in the solutions of the amine-containing polymer and the suspension of nanodiamond are continued until the desired number of nanodiamond layers is formed around the microdiamond. Finally, the core−shell particles are cross-linked with 1,2,5,6-diepoxycyclooctane or reacted with 1,2-epoxyoctadecane. Layer-by-layer deposition of PAAm and nanodiamond is also studied on planar Si/SiO2 surfaces, which were characterized by scanning electron microscopy (SEM), Rutherford backscattering spect...
TL;DR: An overall picture of proteome changes underlying both nigrostriatal pathways and other brain regions potentially involved in MPTP-induced neurodegeneration is presented, which provides a valuable reference resource for future hypothesis-driven functional studies of PD.
Abstract: Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration in the nigrostriatal region of the brain; however, the neurodegeneration extends well beyond dopaminergic neurons. To gain a better understanding of the molecular changes relevant to PD, we applied two-dimensional LC-MS/MS to comparatively analyze the proteome changes in four brain regions (striatum, cerebellum, cortex, and the rest of brain) using a MPTP-induced PD mouse model with the objective to identify nigrostriatal-specific and other region-specific protein abundance changes. The combined analyses resulted in the identification of 4,895 non-redundant proteins with at least two unique peptides per protein. The relative abundance changes in each analyzed brain region were estimated based on the spectral count information. A total of 518 proteins were observed with significant MPTP-induced changes across different brain regions. 270 of these proteins were observed with specific changes occurring either only in the striatum and/or in the rest of the brain region that contains substantia nigra, suggesting that these proteins are associated with the underlying nigrostriatal pathways. Many of the proteins that exhibit significant abundance changes were associated with dopamine signaling, mitochondrial dysfunction, the ubiquitin system, calcium signaling, the oxidative stress response, and apoptosis. A set of proteins with either consistent change across all brain regions or with changes specific to the cortex and cerebellum regions were also detected. One of the interesting proteins is ubiquitin specific protease (USP9X), a deubiquination enzyme involved in the protection of proteins from degradation and promotion of the TGF-β pathway, which exhibited altered abundances in all brain regions. Western blot validation showed similar spatial changes, suggesting that USP9X is potentially associated with neurodegeneration. Together, this study for the first time presents an overall picture of proteome changes underlying both nigrostriatal pathways and other brain regions potentially involved in MPTP-induced neurodegeneration. The observed molecular changes provide a valuable reference resource for future hypothesis-driven functional studies of PD.
TL;DR: In this article, molecularly chemisorbed O2 species were directly imaged on reduced TiO2(110) at 50 K with high-resolution scanning tunneling microscopy (STM) and two different O2 adsorption channels, bridging oxygen vacancies (VO) and another at 5-fold coordinated terminal titanium atoms (Ti5c), have been identified.
Abstract: Molecularly chemisorbed O2 species were directly imaged on reduced TiO2(110) at 50 K with high-resolution scanning tunneling microscopy (STM). Two different O2 adsorption channels, one at bridging oxygen vacancies (VO) and another at 5-fold coordinated terminal titanium atoms (Ti5c), have been identified. While O2 species at the Ti5c site appears as a single protrusion centered on the Ti5c row, the O2 at VO manifests itself by a disappearance of the VO feature. It is found that the STM tip can easily dissociate O2 species, unless extremely low magnitude of the tunneling parameters are used. The O2 molecules chemisorbed at low temperatures at these two distinct sites are the most likely precursors for the two O2 dissociation channels, observed at temperatures above 150 and 230 K at the VO and Ti5c sites, respectively.
TL;DR: A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine using high-density 16S microarrays (PhyloChip), revealing the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.
Abstract: A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mossbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.
TL;DR: In this paper, the nighttime chemical evolution of aerosol and trace gases in a coal-fired power plant plume was monitored with the Department of Energy Grumman Gulfstream-1 aircraft during the 2002 New England Air Quality Study field campaign.
Abstract: [1] Nighttime chemical evolution of aerosol and trace gases in a coal-fired power plant plume was monitored with the Department of Energy Grumman Gulfstream-1 aircraft during the 2002 New England Air Quality Study field campaign. Quasi-Lagrangian sampling in the plume at increasing downwind distances and processing times was guided by a constant-volume balloon that was released near the power plant at sunset. While no evidence of fly ash particles was found, concentrations of particulate organics, sulfate, and nitrate were higher in the plume than in the background air. The enhanced sulfate concentrations were attributed to direct emissions of gaseous H2SO4, some of which had formed new particles as evidenced by enhanced concentrations of nucleation-mode particles in the plume. The aerosol species were internally mixed and the particles were acidic, suggesting that particulate nitrate was in the form of organic nitrate. The enhanced particulate organic and nitrate masses in the plume were inferred as secondary organic aerosol, which was possibly formed from NO3 radical-initiated oxidation of isoprene and other trace organic gases in the presence of acidic sulfate particles. Microspectroscopic analysis of particle samples suggested that some sulfate was in the form of organosulfates. Microspectroscopy also revealed the presence of sp2 hybridized C = C bonds, which decreased with increasing processing time in the plume, possibly because of heterogeneous chemistry on particulate organics. Constrained plume modeling analysis of the aircraft and tetroon observations showed that heterogeneous hydrolysis of N2O5 was negligibly slow. These results have significant implications for several issues related to the impacts of power plant emissions on air quality and climate.
TL;DR: In this paper, the authors used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus.
Abstract: The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of approximately 6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.
TL;DR: It is shown that raising the separation field by ∼35% over the previous 21 kV/cm provides similar or better resolution (with resolving powers of >200 for multiply charged peptides) using only 50% He, which avoids problems due to elevated pressure and He content in the mass spectrometer.
Abstract: The ion mobility spectrometry (IMS) methods are grouped into conventional IMS, based on the absolute ion mobility, and differential or field asymmetric waveform IMS (FAIMS), based on mobility differences between strong and weak electric fields. A key attraction of FAIMS is substantial orthogonality to mass spectrometry (MS). Although several FAIMS/MS platforms were commercialized, their utility was limited by FAIMS resolving power, typically ∼10−20. Recently, gas mixtures comprising up to 75% He have enabled resolving power >100 that permits separation of numerous heretofore “coeluting” isomers. This performance opens major new proteomic and other biological applications. Here, we show that raising the separation field by ∼35% over the previous 21 kV/cm provides similar or better resolution (with resolving powers of >200 for multiply charged peptides) using only 50% He, which avoids problems due to elevated pressure and He content in the mass spectrometer. The heating of ions by the separation field in th...
TL;DR: It is demonstrated that the active-space CR-EomCCSD(T) corrections lower the EOMCCSD (iterative equation-of-motion coupled-cluster method with singles and doubles) excitation energies by 0.2 and 0.3 eV, which leads to a better agreement with experiment, and the quality of basis sets used is discussed.
Abstract: The completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] has proven to be a reliable tool in describing vertical excitation energies in small and medium size molecules. In order to reduce the high numerical cost of the genuine CR-EOMCCSD(T) method and make noniterative CR-EOMCCSD(T) approaches applicable to large molecular systems, two active-space variants of this formalism [the CR-EOMCCSd(t)-II and CR-EOMCCSd(t)-III methods], based on two different choices of the subspace of triply excited configurations employed to construct noniterative correction, are introduced. In calculations for green fluorescent protein (GFP) and free-base porphyrin, where the CR-EOMCCSD(T) results are available, we show good agreement between the active-space CR-EOMCCSD(T) (variant II) and full CR-EOMCCSD(T) excitation energies. For the oligoporphyrin dimer (P2TA) active-space CR-EOMCCSD(T) results provide reasonable agreement with experimentally inf...
TL;DR: 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.
Abstract: 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.