Showing papers by "Environmental Molecular Sciences Laboratory published in 2008"
TL;DR: The proposed tandem IgY12-SuperMix immunoaffinity separation system separates ∼60 abundant proteins from the low abundance proteins in plasma, allowing for significant enrichment of low abundance plasma proteins in the SuperMix flow-through fraction.
203 citations
TL;DR: A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer product range.
Abstract: Chemical composition of secondary organic aerosol (SOA) formed from the ozone-initiated oxidation of limonene is characterized by high-resolution electrospray ionization mass spectrometry in both positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z 300) condensed products of oxidation. A combination of high resolving power (m/Δm ∼ 60 000) and Kendrick mass defect analysis makes it possible to unambiguously determine the molecular composition of hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O : C ratios of 0.43 and 0.50 determined from the positive and negative ion mode spectra, respectively. A possible reaction mechanism for the formation of the first generation SOA molecular components is considered. The discussed mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene. In addition, it includes isomerization and decomposition pathways for alkoxy radicals resulting from unimolecular decomposition of carbonyl oxides that have been disregarded by previous studies. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C–C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer product range.
151 citations
TL;DR: A probabilistic clustering model is developed that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner and reveals a complex relationship between transcriptome and proteome.
Abstract: Motivation: Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated.
Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC). The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the Gene Ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding.
Availability: Matlab code is available from the authors on request.
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.
145 citations
TL;DR: In this article, four authentic mineral dust source materials (SB, Inland Saudi sand (IS), Saharan Sand (SS) and China Loess (CL)) and one commercial reference material (AZTD) were spectroscopically characterized, and their dissolution at pH 1 was examined in aqueous batch systems.
Abstract: Processes that solubilize the iron in mineral dust aerosols may increase the amount of iron supplied to ocean surface waters, and thereby stimulate phytoplankton productivity. It was recently proposed that mixing of mineral dusts with SO2 and HNO3 produces extremely acidic environments that favor the formation of bioavailable Fe(II). Here, four authentic mineral dust source materials (Saudi Beach sand (SB), Inland Saudi sand (IS), Saharan Sand (SS) and China Loess (CL)) and one commercial reference material (Arizona Test Dust (AZTD)) were spectroscopically characterized, and their dissolution at pH 1 was examined in aqueous batch systems. Spectroscopic analyses indicated that the bulk and near-surface region of all samples possessed similar elemental compositions and that iron was unevenly distributed among dust 10 particles. Mossbauer spectroscopy revealed Fe(III) in all samples, although SB, CL and AZTD also contained appreciable Fe(II). Both Fe(II) and Fe(III) were primarily substituted into aluminosilicates, although CL, AZTD and IS also contained Fe(III) oxides. Total iron solubility (defined as the summed concentration of dissolved Fe(II) and Fe(III) measured after 24 h) ranged 14 between 4-12% of the source materials’ iron content, but did not scale with either the surface area or the iron content of the samples. This suggestsmore » that other factors such as iron speciation and mineralogy may play a key role in iron solubility. Also, the elevated nitrate concentrations encountered from nitric acid at pH 1 suppressed dissolution of Fe(II) from AZTD, CL and SB particles, which we propose results from the surface-mediated, non-photochemical reduction of nitrate by Fe(II).« less
143 citations
TL;DR: This system performs multiple LC separations in parallel, but staggers each of them such that the data-rich region of each separation is sampled sequentially, which maximizes the use of the mass spectrometer.
Abstract: We describe a four-column, high-pressure capillary liquid chromatography (LC) system for robust, high-throughput liquid chromatography−mass spectrometry (LC−MS(/MS)) analyses. This system performs multiple LC separations in parallel, but staggers each of them such that the data-rich region of each separation is sampled sequentially. By allowing nearly continuous data acquisition, this design maximizes the use of the mass spectrometer. Each analytical column is connected to a corresponding ESI emitter in order to avoid the use of postcolumn switching and associated dead volume issues. Encoding translation stages are employed to sequentially position the emitters at the MS inlet. The high reproducibility of this system is demonstrated using consecutive analyses of global tryptic digest of the microbe Shewanella oneidensis.
133 citations
TL;DR: In this article, the long-term (>200 day) removal efficiency of uranium from a simulated groundwater during biostimulation with an electron donor (3 mM acetate) under low sulfate conditions was evaluated.
122 citations
TL;DR: It is suggested that proteins whose functions should be further investigated in order to better understand the mechanisms of electron transport to Fe(III) oxide in G. sulfurreducens requires additional and/or different proteins than electron transfer to soluble, chelated Fe(II) oxide.
121 citations
TL;DR: In this paper, the reduction of uranium(VI) by Shewanella oneidensis MR-1 was studied to examine the effects of bioreduction kinetics and background electrolyte on the physical properties and reactivity to reoxidation of the biogenic uraninite, UO 2(s).
119 citations
TL;DR: In this paper, a combination of tools for routine analysis including X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and x-ray diffraction (XRD) are used to obtain essential information.
Abstract: Nanostructured materials are increasingly subject to nearly every type of chemical and physical analysis possible. Due to their small sizes, there is a significant focus on tools with high spatial resolution. It is also natural to characterize nanomaterials using tools designed to analyze surfaces, because of their high surface area. Regardless of the approach, nanostructured materials present a variety of obstacles to adequate, useful, and needed analysis. Case studies of measurements on ceria and iron metal-core/oxide-shell nanoparticles are used to introduce some of the issues that frequently need to be addressed during analysis of nanostructured materials. We use a combination of tools for routine analysis including X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and x-ray diffraction (XRD) and apply several other methods as needed to obtain essential information. The examples provide an introduction to other issues and complications associated with the analysis of nanostructured materials including particle stability, probe effects, environmental effects, specimen handling, surface coating, contamination, and time. Copyright © 2008 John Wiley & Sons, Ltd.
117 citations
TL;DR: In this paper, free and bound EPS produced by suspended cultures of Escherichia coli and Serratia marcescens were characterized in detail using colorimetric analysis of total proteins and polysaccharides, Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectrography (XPS), and Auger electron spectrograms (AES) in the presence and absence of bismuth-based antifouling agents.
115 citations
TL;DR: The application of microscopic Fourier transform infrared (micro-FT-IR) spectroscopy combined with complementary methods of particle analysis is demonstrated here for investigations of phase transitions and hygroscopic growth of micron-sized particles.
Abstract: The application of microscopic Fourier transform infrared (micro-FT-IR) spectroscopy combined with complementary methods of particle analysis is demonstrated here for investigations of phase transitions and hygroscopic growth of micron-sized particles. The approach utilizes the exposure of substrate-deposited, isolated particles to humidified nitrogen inside a sample cell followed by micro-FT-IR spectroscopy over a selected sample area. Phase transitions of NaCl, sea salt, NaNO3, and (NH4)2SO4 particles are monitored with this technique to evaluate its utility and applicability for particle hydration studies. The results are found in excellent agreement with literature data in terms of (a) reliable and reproducible detection of deliquescence and efflorescence phase transitions, (b) quantitative measurements of water-to-solute ratios in particles as a function of relative humidity, and (c) changes in the IR spectra resulting from phase transitions and changing relative humidity. Additional methods of particle analysis are employed to complement and assist in the interpretation of particle hygroscopicity data obtained from micro-FT-IR measurements. The analytical approach and the experimental setup presented here are relatively simple, inexpensive, readily available and therefore may be practical for hydration studies of environmental particles collected in both laboratory and field studies.
TL;DR: In this article, the authors investigated changes in soil carbon cycling with reforestation across a long-term, replicated chronosequence of tropical secondary forests regrowing on abandoned pastures.
TL;DR: High resolution ESI-MS showed that reactions of carbonyls with methanol produce significant amounts of hemiacetals and acetals on time scales ranging from several minutes to several days, with the reaction rates increasing in acidified solutions.
Abstract: This study examined the effect of solvent on the analysis of organic aerosol extracts using electrospray ionization mass spectrometry (ESI-MS). Secondary organic aerosol (SOA) produced by ozonation of d-limonene, as well as several organic molecules with functional groups typical for OA constituents, were extracted in methanol, d3-methanol, acetonitrile, and d3acetonitrile to investigate the extent and relative rates of reactions between analyte and solvent. High resolution ESIMS showed that reactions of carbonyls with methanol produce significant amounts of hemiacetals and acetals on time scales ranging from several minutes to several days, with the reaction rates increasing in acidified solutions. Carboxylic acid groups were observed to react with methanol resulting intheformationofesters.Incontrast,acetonitrileextractsshowed no evidence of reactions with analyte molecules, suggesting that acetonitrile is the preferred solvent for SOA extraction. The use of solvent-analyte reactivity as a tool for the improved characterizationoffunctionalgroupsincomplexorganicmixtures was demonstrated. Direct comparison between mass spectra of the same SOA samples extracted in methanol versus acetonitrile was used to estimate the lower limits for the relative fractions of carbonyls (g42%) and carboxylic acids (g55%) in d-limonene SOA.
TL;DR: In this paper, the analysis of individual particles sampled from air masses that originated over the open ocean and then passed through the area of the California current located along the northern California coast was performed.
Abstract: [1] Detailed chemical speciation of the dry residue particles from individual cloud droplets and interstitial aerosol collected during the Marine Stratus Experiment (MASE) was performed using a combination of complementary microanalysis techniques. Techniques include computer controlled scanning electron microscopy with energy dispersed analysis of X rays (CCSEM/EDX), time-of-flight secondary ionization mass spectrometry (TOF-SIMS), and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS). Samples were collected at the ground site located in Point Reyes National Seashore, approximately 1 km from the coast. This manuscript focuses on the analysis of individual particles sampled from air masses that originated over the open ocean and then passed through the area of the California current located along the northern California coast. On the basis of composition, morphology, and chemical bonding information, two externally mixed, distinct classes of sulfur containing particles were identified: chemically modified (aged) sea salt particles and secondary formed sulfate particles. The results indicate substantial heterogeneous replacement of chloride by methanesulfonate (CH3SO3−) and non-sea-salt sulfate (nss-SO42−) in sea-salt particles with characteristic ratios of nss-S/Na > 0.10 and CH3SO3−/nss-SO42− > 0.6.
TL;DR: A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5-35 kpsi was demonstrated for proteomic analysis and advantages include greatly simplified sample processing, easy implementation, no cross contamination among samples, and cost effectiveness.
Abstract: A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5−35 kpsi was demonstrated for proteomic analysis. Successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. Method performance in terms of the number of Shewanella oneidensis peptides and proteins identified in a shotgun approach was evaluated relative to a traditional “overnight” sample preparation method. Advantages of the new method include greatly simplified sample processing, easy implementation, no cross contamination among samples, and cost effectiveness.
TL;DR: First principles molecular dynamics simulations of the hydration shells surrounding UO(2)(2+) ions are reported for temperatures near 300 K, finding the bonding pattern substantially returned to the tetrahedral structure of bulk water.
Abstract: First principles molecular dynamics simulations of the hydration shells surrounding UO(2)(2+) ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average U=O bond length was found to be 1.77 A. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 A (2.46 A, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59 A. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO(2)(2+) ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO(2)(2+), oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.
TL;DR: In this article, the photooxidation of alpha-pinene in the presence of increasing concentrations of NO2 was studied in a Teflon chamber at relative humidities from 70 - 88% and temperatures from 296 - 304 K.
TL;DR: In response to the recent emergence of monkeypox in Africa and the threat of smallpox bioterrorism, two orthopoxviruses with different pathogenic potentials, human monkeypox virus and vaccinia virus, were proteomically compared with the goal of identifying proteins required for pathogenesis.
Abstract: Orthopoxviruses are among the largest and most complex of the animal viruses. In response to the recent emergence of monkeypox in Africa and the threat of smallpox bioterrorism, two orthopoxviruses with different pathogenic potentials, human monkeypox virus and vaccinia virus, were proteomically compared with the goal of identifying proteins required for pathogenesis. Orthopoxviruses were grown in HeLa cells to two different viral forms (intracellular mature virus and extracellular enveloped virus), purified by sucrose gradient ultracentrifugation, denatured using RapiGest™ surfactant, and digested with trypsin. Unfractionated samples and strong cation exchange HPLC fractions were analyzed by high-resolution reversed-phase nano-LC-MS/MS, and analyses of the MS/MS spectra using SEQUEST® and X! Tandem resulted in the confident identification of hundreds of monkeypox, vaccinia, and copurified host-cell proteins. The unfractionated samples were additionally analyzed by LC-MS on an LTQ-Orbitrap™, and the accurate mass and elution time tag approach was used to perform quantitative comparisons. Possible pathophysiological roles of differentially abundant Orthopoxvirus proteins are discussed. Data, processed results, and protocols are available at http://www.proteomicsresource.org/.
TL;DR: The proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits among environmental and pathogenic bacteria.
Abstract: While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.
TL;DR: Global proteome profiling is applied in combination with a neurite purification methodology for comparative analysis of the soma and neurite proteomes of neuroblastoma cells to provide insight into the spatial organization of signaling networks that enable neuritogenesis.
Abstract: Neurite extension and growth cone navigation are guided by extracellular cues that control cytoskeletal rearrangements. However, understanding the complex signaling mechanisms that mediate neuritogenesis has been limited by the inability to biochemically separate the neurite and soma for spatial proteomic and bioinformatic analyses. Here, we apply global proteome profiling in combination with a neurite purification methodology for comparative analysis of the soma and neurite proteomes of neuroblastoma cells. The spatial relationship of 4,855 proteins were mapped, revealing networks of signaling proteins that control integrins, the actin cytoskeleton, and axonal guidance in the extending neurite. Bioinformatics and functional analyses revealed a spatially compartmentalized Rac/Cdc42 signaling network that operates in conjunction with multiple guanine-nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) to control neurite formation. Interestingly, RNA interference experiments revealed that the different GEFs and GAPs regulate specialized functions during neurite formation, including neurite growth and retraction kinetics, cytoskeletal organization, and cell polarity. Our findings provide insight into the spatial organization of signaling networks that enable neuritogenesis and provide a comprehensive system-wide profile of proteins that mediate this process, including those that control Rac and Cdc42 signaling.
TL;DR: The net reaction probability was found to increase with increasing relative humidity, and the apparent, pseudo first-order rate constant for the reaction was determined from oxygen enrichment in individual particles as a function of particle loading.
Abstract: Heterogeneous reaction kinetics of gaseous nitric acid (HNO3) with calcium carbonate (CaCO3) particles was investigated using a particle-on-substrate stagnation flow reactor (PS-SFR). This technique utilizes the exposure of substrate deposited, isolated, and narrowly dispersed particles to a gas mixture of HNO3/H2O/N2, followed by microanalysis of individual reacted particles using computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX). The first series of experiments were conducted at atmospheric pressure, room temperature and constant relative humidity (40%) with a median dry particle diameter of Dp = 0.85 μm, particle loading densities 2 × 104 ≤ Ns ≤ 6 × 106 cm-2 and free stream HNO3 concentrations of 7, 14, and 25 ppb. The apparent, pseudo first-order rate constant for the reaction was determined from oxygen enrichment in individual particles as a function of particle loading. Quantitative treatment of the data using a diffusion-kinetic model yields a lower...
TL;DR: The modified STOMP simulator was able to predict the experimental observed fluid displacing behavior well and might be used to predict subsurface remediation performance when a shear-thinning fluid is used to remediate a heterogeneous system at larger scales.
TL;DR: A subset of highly expressed proteins unique to S. typhi that were exclusively detected under conditions that are thought to mimic the infective state in macrophage cells suggest that this subset of proteins may play a role in S.Typhoid fever pathogenesis and human host specificity.
Abstract: Typhoid fever is a potentially fatal disease caused by the bacterial pathogen Salmonella enterica serotype Typhi (S. typhi). S. typhi infection is a complex process that involves numerous bacterially encoded virulence determinants, and these are thought to confer both stringent human host specificity and a high mortality rate. In the present study, we used a liquid chromatography–mass spectrometry (LC−MS)-based proteomics strategy to investigate the proteome of logarithmic, stationary phase, and low pH/low magnesium (MgM) S. typhi cultures. This represents the first large-scale comprehensive characterization of the S. typhi proteome. Our analysis identified a total of 2066 S. typhi proteins. In an effort to identify putative S. typhi-specific virulence factors, we then compared our S. typhi results to those obtained in a previously published study of the S. typhimurium proteome under similar conditions (Adkins, J. N. et al. Mol. Cell. Proteomics 2006, 5, 1450−1461). Comparative proteomics analysis of S. t...
TL;DR: A 2:1 molar ratio preparation of bismuth with a lipophilic dithiol significantly reduced extracellular polymeric substances (EPS) expression by Brevundimonas diminuta in suspended cultures at levels just below the minimum inhibitory concentration (MIC).
Abstract: A 2:1 molar ratio preparation of bismuth with a lipophilic dithiol (3-dimercapto-1-propanol, BAL)significantly reduced extracellular polymeric substances (EPS) expression by Brevundimonas diminuta in suspended cultures at levels just below the minimum inhibitory concentration (MIC). Total polysaccharides and proteins secreted by B. diminuta decreased by approximately 95% over a 5-day period when exposed to the bismuth-BAL chelate (BisBAL) at near MIC (12 μM). Fourier-transform infrared spectroscopy (FTIR) suggested that a possible mechanism of biofilm disruption by BisBAL is the inhibition of carbohydrate Oacetylation. FTIR also revealed extensive homology between EPS samples with and without BisBAL treatment, with proteins, polysaccharides, and peptides varying predominantly only in the amount expressed. EPS secretion decreased following BisBAL treatment as verified by atomic force microscopy and scanning electron microscopy. Without BisBAL treatment, a slime-like EPS matrix secreted by B. diminuta resulted in biofouling and inefficient hydrodynamic backwashing of microfiltration membranes.
TL;DR: It is demonstrated that within a single cell type, the EG FR autocrine system can couple multiple signaling pathways to ERK activation and that this modulation of EGFR autocrine signaling can be accomplished at multiple regulatory steps.
TL;DR: An efficient on-line digestion system that reduces the number of sample manipulation steps and offers a powerful approach for high-throughput screening of proteins that could prove valuable in biochemical research (rapid screening of protein-based drugs).
Abstract: An efficient on-line digestion system that reduces the number of sample manipulation steps has been demonstrated for high-throughput proteomics. By incorporating a pressurized sample loop into a liquid chromatography-based separation system, both sample and enzyme (e.g., trypsin) can be simultaneously introduced to produce a complete, yet rapid digestion. Both standard proteins and a complex Shewanella oneidensis global protein extract were digested and analyzed using the automated online pressurized digestion system coupled to an ion mobility time-of-flight mass spectrometer, an ion trap mass spectrometer, or both. The system denatured, digested, and separated product peptides in a manner of minutes, making it amenable to on-line high-throughput applications. In addition to simplifying and expediting sample processing, the system was easy to implement and no cross-contamination was observed among samples. As a result, the online digestion system offers a powerful approach for high-throughput screening of...
TL;DR: This work provides the first comprehensive proteomic characterization of pancreatic islets for mouse, the most commonly used animal model in diabetes research, and identifies a unique set of proteins, in addition to those with known functions such as peptide hormones secreted from the islets, contains several proteins with as yet unknown functions.
Abstract: The pancreatic islets of Langerhans, and especially the insulin-producing beta cells, play a central role in the maintenance of glucose homeostasis. Alterations in the expression of multiple proteins in the islets that contribute to the maintenance of islet function are likely to underlie the pathogenesis of types 1 and 2 diabetes. To identify proteins that constitute the islet proteome, we provide the first comprehensive proteomic characterization of pancreatic islets for mouse, the most commonly used animal model in diabetes research. Using strong cation exchange fractionation coupled with reversed phase LC-MS/MS we report the confident identification of 17,350 different tryptic peptides covering 2612 proteins having at least two unique peptides per protein. The data set also identified approximately 60 post-translationally modified peptides including oxidative modifications and phosphorylation. While many of the identified phosphorylation sites corroborate those previously known, the oxidative modifications observed on cysteinyl residues reveal potentially novel information suggesting a role for oxidative stress in islet function. Comparative analysis with 15 available proteomic data sets from other mouse tissues and cells revealed a set of 133 proteins predominantly expressed in pancreatic islets. This unique set of proteins, in addition to those with known functions such as peptide hormones secreted from the islets, contains several proteins with as yet unknown functions. The mouse islet protein and peptide database accessible at (http://ncrr.pnl.gov), provides an important reference resource for the research community to facilitate research in the diabetes and metabolism fields.
TL;DR: Electronic structure calculations at the coupled cluster (CCSD(T) and density functional theory levels with relativistic effective core potentials and large basis sets were used to predict the isolated uranyl ion frequencies to calibrate the UO22+ results.
Abstract: Electronic structure calculations at the coupled cluster (CCSD(T)) and density functional theory levels with relativistic effective core potentials and large basis sets were used to predict the isolated uranyl ion frequencies. The effects of anharmonicity and spin−orbit corrections on the harmonic frequencies were calculated. The anharmonic effects are larger than the spin−orbit corrections, but both are small. The anharmonic effects decreased all the frequencies, whereas the spin−orbit corrections increased the stretches and decreased the bend. Overall, these two corrections decreased the harmonic asymmetric stretch frequency by 6 cm-1, the symmetric stretch by 3 cm-1, and the bend by 3 cm-1. The best calculated values for UO22+ for the asymmetric stretch, symmetric stretch, and bend were 1113, 1032, and 174 cm-1, respectively. The separation between the asymmetric and the symmetric stretch band origins was predicted to be 81 cm-1, which is consistent with experimental trends for substituted uranyls in s...
TL;DR: In this paper, the adsorption and photoreactivity of an organic adlayer, trimethyl acetate (TMA), on structurally excellent anatase (001) epitaxial thin films grown by oxygen plasma assisted molecular beam epitaxy (OPAMBE).
Abstract: Surfaces of titanium dioxide in both rutile and anatase polymorphs have attracted significant attention in catalysis and photochemistry. The (110) orientation of rutile, and to a lesser extent other rutile orientations, have been studied on an atomic scale, yielding information on surface structure and chemical reactivity. In contrast, the thermal and photochemistry of well-defined, single-crystal anatase surfaces has not been investigated, largely because of the metastable nature of anatase, as well as the lack of availability of high-quality surfaces. Here we describe a study of the adsorption and photoreactivity of an organic adlayer, trimethyl acetate (TMA), on structurally excellent anatase (001) epitaxial thin films grown by oxygen plasma assisted molecular beam epitaxy (OPAMBE). High-resolution scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and photodesorption spectrometry have been used to study the chemisorption and ultraviolet (UV) light-induced photodecomposition o...
TL;DR: The unfolding of compact ubiquitin ion geometries as a function of waveform amplitude (dispersion field, E(D)) and gas temperature, T and isomerization of ions in FAIMS appears to be determined by the excitation at waveform peaks.
Abstract: Field asymmetric waveform ion mobility spectrometry (FAIMS) has emerged as an analytical tool of broad utility, especially in conjunction with mass spectrometry. Of particular promise is the use of FAIMS and 2-D ion mobility methods that combine FAIMS with conventional IMS to resolve and characterize protein and other macromolecular conformers. However, FAIMS operation requires a strong electric field, and ions are inevitably heated by energetic collisions with buffer gas molecules. This may induce ion isomerization or dissociation, which distort the separation properties of FAIMS (and subsequent stages) or reduce instrumental sensitivity. As FAIMS employs a periodic waveform, whether those processes are controlled by ion temperature at maximum or average field intensity has been debated. Here we address this issue by measuring the unfolding of compact ubiquitin ion geometries as a function of waveform amplitude (dispersion field, ED) and gas temperature, T. The field heating is quantified by matching the...