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The reactions of PH(n)+ ions (n = 0-3) were examined with a number of neutrals using ion-cyclotron-resonance techniques. The reactions examined have significance for the distribution of phosphorus in interstellar molecules. The results indicate that interstellar molecules containing the P-O bond are likely to be more abundant than those containing the P-H bond.
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The dynamic behaviour of floating offshore wind turbines (FOWTs) involves complex interactions of multivariate loads from wind, waves, and currents, which result in complex motion characteristics. Although methods for analysing global motion responses are well-established, the time- and location-dependent kinematics remain underexplored. This paper investigates the instantaneous centre of rotation (ICR), a point of zero velocity at a time instance of general plane motion. Understanding and strategically positioning the ICR can reduce the dynamic motion in critical structural locations, enhancing the performance and structural robustness of FOWTs. The paper presents a method for computing the ICR using time-domain simulation results and proposes a statistical analysis approach suitable for design studies. Building on prior research, it examines the sensitivity of the ICR to external loading and design features, providing insights into how these factors influence motion response and how the motion response influences the statistics of the ICR, structural loads, and other performance metrics of interest. The study explores two FOWT configurations, a spar and a semisubmersible, identifying design variables that most effectively control the ICR statistics and identifying the ICR statistics most correlated with the responses of interest. Finally, through two case studies, we demonstrate how to apply these new insights in a practical design scenario. By adjusting the design variables most correlated with the ICR (fairlead vertical position and centre of mass for the spar and mooring line length and offset column diameter for the semisubmersible), we successfully modified the designs of the floating support structures to reduce the loads in the mooring lines, tower base, and blade roots, improving the ultimate strength and fatigue characteristics compared to the original designs.
The development of the phase-imaging ion-cyclotron resonance (PI-ICR) technique for use in Penning trap mass spectrometry (PTMS) increased the speed and precision with which PTMS experiments can be carried out. In PI-ICR, data sets of the locations of individual ion hits on a detector are created showing how ions cluster together into spots according to their cyclotron frequency. Ideal data sets would consist of a single, 2D-spherical spot with no other noise, but in practice data sets typically contain multiple spots, non-spherical spots, or significant noise, all of which can make determining the locations of spot centers non-trivial. A method for assigning groups of ions to their respective spots and determining the spot centers is therefore essential for further improving precision and confidence in PI-ICR experiments. Here, we present the class of Gaussian mixture model (GMM) clustering algorithms as an optimal solution. We show that on simulated PI-ICR data, several types of GMM clustering algorithms perform better than other clustering algorithms over a variety of typical scenarios encountered in PI-ICR. The mass spectra of 163Gd, 163 mGd, 162 Tb, and 162 mTb measured using PI-ICR at the Canadian Penning trap mass spectrometer were checked using GMMs, producing results that were in close agreement with the previously published values.
Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.
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Nanochannel-based fluidic diodes display ion selectivity and ion-current rectification (ICR), which may prove important in energy harvesting and biosensors. This paper reports asymmetric functionalization of the outer surface of a flexible nanochannel polymer membrane to create fluidic diodes that give ICR. Layer-by-layer (LbL) adsorption with cross-linking of only the underlying part of the polyelectrolyte nanofilm leads to a porosity step across the film. The combination of a high effective surface-charge density and the porosity step in the film leads to a remarkable maximum ICR factor of ~200 with a pH gradient across the film. Incorporation of pH-sensitive polyelectrolyte components enables the ICR factor to increase an order of magnitude on going from pH 8 to pH 3. Furthermore, the coated membrane shows excellent anion-selectivity. Thus, LbL adsorption with partial cross-linking provides a simple method for creating coated nanochannel membranes that serve as pH-responsive ionic diodes for potential chemical/biosensors.
The measured atmospheric parameters and the fluxes of latent and sensible heat across the biosphere-atmosphere interface collected during the water-stressed period of the First ISLSCP Field Experiment (FIFE) were compared with those calculated by an experimental version of the Biosphere-Atmosphere Transfer Scheme (Ex-BATS). It is shown that the brightness temperature (T(B)) values observed near the surface during FIFE 1987 are closely correlated to in-canopy temperatures calculated by Ex-BATS. The 1987 near-surface observations of T(B) are also well correlated to AVHHR channels 4 and 5 measurements. An inverted form of Ex-BATS was applied to determine the associated required in-canopy temperatures, T(icr), and regressions between T(icr) and T(B) found from the 1987 data were applied to the 1989 observed T(B) at a different site. The T(icr) so estimated showed excellent correlation to the 1989 model calculated T(icr).
The reaction of the methyl cation with hydrogen cyanide is revisited. We have confidence that we have resolved a long standing apparent contradiction of experimental results. A literature history is presented along with one new experiment and a re-examination of an old experiment. In this present work it is shown that all of the previous studies had made consistent observations. Yet, each of the previous studies failed to observe all of the information present. The methyl cation does react with HCN by radiative association, a fact which had been in doubt. The product ions formed in the two-body and three-body processes react differently with HCN. The collisionally stabilized association product formed by a three-body mechanism, does not react with HCN and is readily detected in the experiments. The radiatively stabilized association product, formed by a slow two-body reaction, is not detected because it reacts with HCN by a fast proton transfer reaction forming the protonated HCN ion. Previous studies either 'lost' this product in the extremely large protonated HCN signal that is always present when HCN is used, or discounted it for various reasons. We have been able to show by ion cyclotron resonance (ICR) techniques (both FT-ICR and tandem ICR-dempster-ICR) that the radiative association product does react with the HCN to form the protonated HCN ion.
Here, we present a detailed molecular characterization of organophosphorus compounds in ambient organic aerosol influenced by wildfire smoke. Biomass burning organic aerosol (BBOA) is an important source of phosphorus (P) to surface waters, where even a small imbalance in the P flux can lead to substantial effects on water quality, such as eutrophication, algal blooms, and oxygen depletion. We aimed to exploit the ultrahigh resolving power, mass accuracy, and sensitivity of Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the molecular composition of an ambient BBOA sample collected downwind of Pacific Northwest wildfires. The 21-T FT-ICR MS yielded 10533 distinct formulae, which included molecular species comprising C, H, O, and P with or without N, i.e., organophosphorus compounds that have long been quantified in wildfire smoke but have not yet been characterized at the molecular level. The lack of detailed molecular characterization of organophosphorus compounds in BBOA is primarily due to their inherently low concentrations in aerosols and poor ionization efficiency in complex mixtures. We demonstrate that the exceptional sensitivity of the 21-T FT-ICR MS allows qualitative analysis of a previously uncharacterized fraction of BBOA without its selective concentration from the organic matrix, exemplifying the need for ultrahigh-resolution tools for a more detailed and accurate molecular depiction of such complex mixtures.
Analysis of proteins and complexes under native mass spectrometric (MS) and solution conditions was typically performed using time-of-flight (ToF) analyzers, due to their routine high m/z transmission and detection capabilities. However, over recent years, the ability of Orbitrap-based mass spectrometers to transmit and detect a range of high molecular weight species is well documented. Herein, we describe how a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (15 T FT-ICR MS) is more than capable of analyzing a wide range of ions in the high m/z scale (>5000), in both positive and negative instrument polarities, ranging from the inorganic cesium iodide salt clusters; a humanized IgG1k monoclonal antibody (mAb; 148.2 kDa); an IgG1-mertansine drug conjugate (148.5 kDa, drug-to-antibody ratio; DAR 2.26); an IgG1-siRNA conjugate (159.1 kDa; ribonucleic acid to antibody ratio; RAR 1); the membrane protein aquaporin-Z (97.2 kDa) liberated from a C8E4 detergent micelle; the empty MSP1D1-nanodisc (142.5 kDa) and the tetradecameric chaperone protein complex GroEL (806.2 kDa; GroEL dimer at 1.6 MDa). We also investigate different regions of the FT-ICR MS that impact ion transmission and desolvation. Finally, we demonstrate how the transmission of these species and resultant spectra are highly consistent with those previously generated on both quadrupole-ToF (Q-ToF) and Orbitrap instrumentation. This article serves as an impactful example of how FT-ICR mass analyzers are competitive to Q-ToFs and Orbitraps for high mass detection at high m/z.
These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME). File formats and software needed to access files: 16S rRNA gene amplicon data: These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported: 1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel. 2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit. 3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format 4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file format FTICR-MS data: 1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format 2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format 3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format
The VASIMR space propulsion development effort relies on a high power (greater than 10kW) helicon source to produce a dense flowing plasma (H, D and He) target for ion cyclotron resonance (ICR) acceleration of the ions. Subsequent expansion in an expanding magnetic field (magnetic nozzle) converts ion lunetic energy to directed momentum. This plasma source must have critical features to enable an effective propulsion device. First, it must ionize most of the input neutral flux of gas, thus producing a plasma stream with a high degree of ionization for application of ICR power. This avoids propellant waste and potential power losses due to charge exchange. Next, the plasma stream must flow into a region of high magnetic field (approximately 0.5 T) for efficient ICR acceleration. Third, the ratio of input power to plasma flux must be low, providing an energy per ion-electron pair approaching 100 eV. Lastly, the source must be robust and capable of very long life-times (years). In our helicon experiment (VX-10) we have measured a ratio of input gas to plasma flux near 100%. The plasma flows from the helicon region (B approximately 0.1 T) into a region with a peak magnetic field of 0.8 T. The energy input per ion-electron pair has been measured at 300 plus or minus 100 eV. Recent results at Oak Ridge National Laboratory (ORNL) show an enhanced efficiency mode of operation with a high power density, over 5 kW in a 5 cm diameter tube. Our helicon is presently 9 cm in diameter and operates up to 3.5 kW of input power. An upgrade to a power level of 10 kW is underway. Much of our recent work has been with a Boswell double-saddle antenna design. We are also converting the antenna design to a helical type. With these modifications, we anticipate an improvement in the ionization efficiency. This paper presents the results from scaling the helicon in the VX-10 device from 3.5 to 10 kW. We also compare the operation with a double-saddle to a helical antenna design. Finally, we discuss modeling of these configurations using ORNL's EMIR code.
This dataset includes characterization data collected on sediment samples from Meander C as part of the Watershed Function Scientific Focus Area (SFA) located in the Upper Colorado River Basin. The data were collected to investigate the nature of mineral-organic associations across the meander transect and with depth. Samples were collected in 2017, and analyzed using sequential extractions (water, pyrophosphate, HCl, and dithionite) and density fractionation. Data collected include: texture, pH, root biomass, and metals (Fe, Al, Ca, Si) of bulk sediment samples; C and N of heavy fraction; and extractable OC, Fe, and Al, and organic matter characterization using high-resolution mass spectrometry (FT-ICR-MS) of sequential extractions. Sample locations are included in the ‘sample_metadata.xlsx” file. Sediment characterization data is included in the accompanying csv files: bulk and density fractions (MCB2017_density-and-bulk-fractions.csv), sequential extractions (MCB2017_sequential-extractions.csv), and FT-ICR-MS data from sequential extractions in three files to be read by the R package ftmsRanalysis (MCB2017_FTICRMS-sequential-edata.csv, MCB2017_FTICRMS-sequential-emeta.csv, and MCB2017_FTICRMS-sequential-fdata.csv). Sediment was collected in triplicate; ID’s refer to individual samples.
Organic C has many benefits for soil, but it is depleted by tillage and crop harvest, and especially so for biofuel crops. Accordingly, strategies such as partially retaining stover or planting a cover crop can help ameliorate the negative effect of C removal. We used a long-term field experiment to study the impacts of stover retention and planting cover crop on soil organic matter (SOM), its extractable components and the soil microbial community. SOM chemical composition characterization was determined by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sequential water, methanol (MeOH), and chloroform (CHCl3) extracts. The characteristics of the soil bacterial community were measured by phospholipid fatty acid (PLFA), real-time quantitative PCR, and 16S rRNA gene sequence. The variations in total SOM content, total microbial biomass, and bacterial population were slight among treatments, but SOM chemical compounds, arbuscular mycorrhizal fungi (AMF) biomass, and bacterial structure changed significantly, and especially so in the coupled application of stover retention and cover crop. Specifically, stover retention enriched more lignin-like compounds in soil, whereas cover crop enriched more condensed hydrocarbons, and had more compounds with an aromaticity index (AI) >0.5. The bacterial community was not altered by the cover crop, but the corn stover retention increased the relative abundances of Myxococcales (Deltaproteobacteria) and decreased that of Actinobacteria. Redundancy analysis (RDA) further unveiled that the bacterial community in the stover treatments had significantly positive association with CHCl3-extracted chemical classes, i.e. unsaturated hydrocarbon and lipid with the coupled application (stover and cover crop), and lignin and protein with the single corn stover treatment. Taken together, our study shows how different C addition practices influence the molecular composition of SOM and the structure of soil microbial communities.
Among the most prominent challenges for the analysis of biomass pyrolysis products is the characterization of the abundant oligomer fraction of bio-oil. This fraction is principally made up of pyrolytic lignins and dehydrated, highly modified sugar oligomers, called humins, in liquid phase. An emerging technique for analysis of this oligomer fraction is high-resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS), which allows for accurate determination of C x H y O z formulae for detected oligomers. Additionally, using simple dehydration and fragmentation reaction schemes, similar formulae can be developed from cellulose-, hemicellulose- and lignin-derived oligomers, which are primary depolymerization products. In this paper, FT-ICR MS analysis is coupled with combinatoric dehydration and fragmentation modeling in order to match experimentally detected bio-oil oligomers with hypothetical pathways for their formation during pyrolysis. In this way, we present a novel strategy by which oligomeric structures can be proposed for bio-oils. Using this approach, it becomes possible to advance the understanding of both the molecular structures comprising the bio-oil oligomer fraction and the pathways by which these structures form during biomass pyrolysis reactions.
The pyrolysis of lignocellulosic materials is a promising technique to produce fuels and chemicals. It is well known that the most abundant products of lignin pyrolysis are oligomeric molecules, known as pyrolytic lignin (PL). The chemical composition of PL has been extensively studied; however, there is still an important debate whether these oligomers are produced directly from the lignin or from the recombination of monomeric pyrolytic products. Existing theories are unable to describe the effect of vacuum on the distribution of pyrolysis products. Hybrid poplar milled wood lignin (MWL) was initially isolated and thoroughly characterized by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Chemical formulas were assigned to each oligomeric compound detected. The MWL was also subjected to vacuum pyrolysis in a modified pyroprobe at 250, 750, and 1000 mbar (absolute pressure), and the resulting liquid products were analyzed by FT-ICR MS. A new strategy to assign structural representations to the oligomeric PL products is proposed, based on the plausible pyrolysis reaction mechanisms of depolymerization/fragmentation applied to original MWL oligomer formulas. Our results support the hypothesis that PL is formed from the removal of moieties from primary lignin pyrolysis products with between three and five aromatic rings. This depolymerization/fragmentation allows the oligomers to reduce their molecular weights to the point where they can be removed from the reaction zone by direct vaporization. Furthermore, this phenomenon highlights the importance of pressure on removal mechanisms and their impact on the molecular weight of the resulting products from lignin pyrolysis.