Distribution Of Compound Classes Research Articles

Mapping of specialized metabolite terms onto a plant phylogeny using text mining and large language models.

Plants produce a staggering array of chemicals that are the basis for organismal function and important human nutrients and medicines. However, it is poorly defined how these compounds evolved and are distributed across the plant kingdom, hindering a systematic view and understanding of plant chemical diversity. Recent advances in plant genome/transcriptome sequencing have provided a well-defined molecular phylogeny of plants, on which the presence of diverse natural products can be mapped to systematically determine their phylogenetic distribution. Here, we built a proof-of-concept workflow where previously reported diverse tyrosine-derived plant natural products were mapped onto the plant tree of life. Plant chemical-species associations were mined from literature, filtered, evaluated through manual inspection of over 2500 scientific articles, and mapped onto the plant phylogeny. The resulting "phylochemical" map confirmed several highly lineage-specific compound class distributions, such as betalain pigments and Amaryllidaceae alkaloids. The map also highlighted several lineages enriched in dopamine-derived compounds, including the orders Caryophyllales, Liliales, and Fabales. Additionally, the application of large language models, using our manually curated data as a ground truth set, showed that post-mining processing can largely be automated with a low false-positive rate, critical for generating a reliable phylochemical map. Although a high false-negative rate remains a challenge, our study demonstrates that combining text mining with language model-based processing can generate broader phylochemical maps, which will serve as a valuable community resource to uncover key evolutionary events that underlie plant chemical diversity and enable system-level views of nature's millions of years of chemical experimentation.

Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy.

In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.IMPORTANCEInfrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus Paxillus involutus at the interface between individual fungal hyphae and cellulose substrates.

The effect of biodegradation on bound aromatic hydrocarbons released from intermediate-temperature gold-tube pyrolysis of severely biodegraded Athabasca bitumen

Polycyclic aromatic hydrocarbons (PAHs) from two severely biodegraded Athabasca oil sand bitumens released by gold-tube pyrolysis at 300–525 °C with 2 °C/h heating rate were characterized by gas chromatography-mass spectrometry. Alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophenes were fully removed by biodegradation from the free phase aromatic hydrocarbon fraction in raw bitumens, while tetracyclic aromatics were partially attacked. Sample A has suffered less extensive biodegradation influence than sample B due to different oil-water-contact situations. Pronounced changes were observed in the distribution of various compound classes after pyrolysis due to thermal cracking, aromatization and condensation. PAHs released from occluded phase at intermediate–temperature (< 425 °C) exhibit clear biodegradation impact. The proportion of alkylnaphthalenes released in initial pyrolysates is much lower than those highly fused aromatics, reflecting more biodegradation influence on lower ring number aromatic hydrocarbons. Within alkylnaphthalenes, naphthalene and methylnaphthalenes with less substituents are largely depleted in the pyrolysates, indicating preferential removal of less alkylated homologues from the occluded phase by biodegradation. Isomer selectivity from the occluded aromatic hydrocarbons follows the same sequences as those observed from the free phase, resulting in poor correlation between isomerization based maturity parameters and heating temperatures. PAHs released from extremely biodegraded bitumens in intermediate–temperature pyrolysates might differ totally from those in the non-degraded oils. Caution should be taken when molecular parameters derived from occluded phase are applied for organic source input and maturity assessment.

High-Resolution Molecular-Level Characterization of a Blanket Bog Peat Profile

To understand peatland carbon-cycling processes ultimately requires the ability to track changes occurring on the molecular-level. In this study, we profile a peat core taken from the world's largest blanket bog, Flow Country, Scotland, using physicochemical properties, ATR-FTIR, solid/liquid-state NMR, and solid/liquid-state FT-ICR-MS. Air-dried peat and labile and recalcitrant peat extracts, including pore water dissolved organic matter (PW-DOM), are analyzed and the merits of each technique are discussed. Solid-state NMR demonstrated changing distribution of compound classes with core depth and water table, the latter not picked up by IR. Liquid-state NMR and MS both demonstrated variations in molecular composition along the core depth in all phases and extracts. Contrary to previous reports, the composition of PW-DOM varied with depth. Major compounds, some previously unreported, identified by 1D/2D NMR occurred throughout the core, suggesting the existence of hot spots of microbial activity/compound accumulation. Offering complementary views, the techniques provided evidence of gradual molecular level changes with age, zonation due to the water table, and hot spots due to microbial activity. This study provides new insights into the molecular signatures of peat layers and establishes the foundation for examining peat function and health at the molecular-level.

Molecular Characterization of Aged Bitumen with Selective and Nonselective Ionization Methods by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. 1. Multiple Pressure Aging Vessel Aging Series

Bitumen is a very complex mixture corresponding to the residue from the vacuum distillation of crude oil. The complexity of such a mixture can be defined by its composition, with several thousand molecules that may contain heteroelements such as sulfur, nitrogen, and oxygen. Almost all bitumen production is used as a binder to produce asphalt pavements. Additional additives or physicochemical treatments can be used to improve the properties and lifetime of this binder. Asphalt pavements are subject to oxidative aging over the years, which leads to deterioration of the physical properties and reduces the performance and durability of the product. To have a better understanding of such mechanisms, artificial techniques can be used to simulate oxidative aging of bitumen. The most-used technique is the pressure aging vessel (PAV) which simulates the long-term aging of bitumens. To characterize oxidative aging at the molecular level, instruments such as Fourier transform ion cyclotron resonance (FTICR) are required. The ultrahigh resolution of this analyzer allows the unambiguous attribution of molecular formulas to each signal. Electrospray ionization (ESI) source was used to selectively ionize acid molecules, while atmospheric pressure photoionization (APPI) source was used to have a nonselective ionization of low-polarity molecules from bitumen. Analyses were carried out on four different PAV aging times (PAV-0h, 25h, 72h, and 96h) to characterize the aging kinetics from a bitumen sample. ESI results allowed the revealing of significant differences from the heteroatom class and family distributions starting from PAV-72h. It was defined by a general decrease of nonoxygenated families (Nx and NxSy) and by an increase of oxygenated families (Oz, NxOz, OzSy, and NxOzSy). The van Krevelen plot evidenced that aging markers correspond to low double bond equivalent (DBE) molecules. The occurrence of aldehydes and fatty acids (DBE 1) with aging in the CHOz family was characterized with DBE versus carbon number plots. Aging markers from OzSy were also characterized with occurrence of benzothiophenic (O2S1) and sulfonic acids (O3S1). Logically, less meaningful results were obtained with APPI. However, this nonselective source allowed the ionization of thiophenes, furans, cycloalkanes, and polycyclic aromatic hydrocarbons that were not observed in ESI measurements. Homogenic decreases in the distribution of nonoxygenated compound classes (HC, S1, S2, and N1) were observed. Concerning the oxygenated molecules, an expansion of the distribution was observed, but without the occurrence of specific aging markers. Oxidation seemed to be favored on linear and naphthenic molecules and not on the highly aromatic ones.

Non‐target screening of leaf litter‐derived dissolved organic matter using liquid chromatography coupled to high‐resolution mass spectrometry (LC‐QTOF‐MS)

AbstractLeaf litter‐derived dissolved organic matter (DOM) is an important source of organic matter entering the mineral soil, but characterization of leaf litter DOM is often not detailed enough to understand DOM dynamics and processes at the molecular level. (Ultra‐) high‐resolution techniques such as Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS), Orbitrap mass spectrometry and quadrupole time‐of‐flight (QTOF) mass spectrometry have brought a new level of detail to (D)OM research by providing molecular formulae and information on molecular structures. We present a novel approach for leaf litter DOM characterization that includes non‐target screening using liquid chromatography (LC) coupled to high‐resolution QTOF‐MS. A method validation test showed that out of 26 spiked naturally occurring DOM molecules in a leaf litter DOM sample, 23 were found as features. After implementation of additional filtering to exclude certain combinations of heteroatoms (that are difficult to resolve even by the newest high‐resolution MS instruments), including molecular formulae with P atoms, 22 molecular formulae were correctly assigned. Although a large part of the annotated molecular formulae was unique for the respective litter sources, the molecular compound class distribution was similar for deciduous, coniferous and mixed leaf litter DOM. Most intense masses were detected in the 100–300 Da mass range, showing a bias of QTOF‐MS towards lower masses compared to FT‐ICR‐MS. The use of LC in combination with QTOF‐MS for leaf litter (D)OM characterization provides, together with Orbitrap‐MS, a more widely available and lower cost high‐resolution MS alternative to FT‐ICR‐MS. Novel approach to the characterization and analysis of leaf litter derived DOM. Non‐target screening using LC‐QTOF‐MS and the patRoon R package. Similar molecular compound class distribution for three leaf litter sources. High‐resolution DOM characterization alternative to FT‐ICR‐MS.Highlights Novel approach to the characterization and analysis of leaf litter‐derived DOM. Non‐target screening using LC‐QTOF‐MS and the patRoon R package. Similar molecular compound class distribution for three leaf litter sources. High‐resolution DOM characterization alternative to FT‐ICR‐MS.

Comparative analyses of cuticular waxes on various organs of faba bean (Vicia faba L.)

Cuticular waxes cover the plant surface and serve as hydrophobic layer, exhibiting various wax profiles between plant species and plant organs. This paper reports comprehensive analysis of the waxes on organs exposed to air, including leaf, stem, pod pericarp, and petals (banner, wing and keel), and on seed coat enwrapped in pod pericarp of faba bean (Vicia faba). In total 7 classes of wax compounds were identified, including fatty acids, primary alcohols, alkyl esters, aldehydes, alkanes, cinnamyl alcohol esters, and alkylresorcinols. Overall, primary alcohols dominated the waxes on leaves and the seed coat enwrapped in pod pericarp, alkanes accumulated largely in stem and petals, whereas alkylresorcinols were observed in leaf, stem and pod pericarp. Organs exposed to air had higher coverage (>1.2 μg/cm2) than those on seed coat (<0.8 μg/cm2), and keel having the highest wax coverage. Meanwhile, the wax coverage on seed coat reduced during the seed development. The variations of wax coverages, compound class distributions and chain length profiles among organs suggested that wax depositions were associated with their ecophysiological functions, and the enzymes involved in wax biosynthesis also showed organ-specific.

Characterization of oil sands naphthenic acids by negative-ion electrospray ionization mass spectrometry: Influence of acidic versus basic transfer solvent

Considerable effort and progress has been made over the past decade with respect to development of analytical tools for the determination of naphthenic acids and related components in environmental samples. However, experimental variables that influence the analytical results have not been fully explored. The relative contributions of Ox classes are of particular interest in data obtained using negative-ion electrospray ionization mass spectrometry. Using two types of ultrahigh resolution mass spectrometers (Orbitrap and FT-ICR), the apparent pH of the transfer solvent was observed to have a significant impact upon compound class distributions. A basic transfer solvent favored the detection of Ox species of lower oxygen content, while acidic pH favored the preferential observation of organic compounds with higher oxygen contents. These observed trends were independent of the instrument type. In addition, when using an acidic transfer solvent, the overall observed response was reduced by a factor of ∼20. Thus, the apparent pH of the transfer solvent has critical influence upon detection and upon the profile of different components observed within a complex mixture. In turn, this significantly impacts oil sands environmental monitoring for toxicity, forensic interpretation, and quantitation; when comparing data sets from different laboratories, these findings should therefore be taken into account.

Using aromatic polyamines with high proton affinity as "proton sponge" dopants for electrospray ionisation mass spectrometry.

Proton sponges are polyamines with high proton affinity that enable gentle deprotonation of even mildly acidic compounds. In this study, the concept of proton sponges as signal enhancing dopants for electrospray ionisation is presented for the first time. 1,8-Bis(dimethylamino)naphthalene (DMAN) and 1,8-bis(tetramethylguanidino)naphthalene (TMGN) were chosen as dopants, using methanol and acetonitrile/methanol as solvents. Individual standard compounds, compound mixtures and a diesel fuel as a complex sample matrix were investigated. Both proton sponges enhanced signal intensities in electrospray ionisation negative mode, but TMGN decomposed rapidly in methanolic solution. Significantly higher signals were only achieved using the acetonitrile/methanol mixture. On average a more than 10-fold higher signal intensity was measured with 10-3 mol l-1 DMAN concentration. A stronger signal increase of alcohol functionalities was observed compared to acid functionalities. All compound classes which were detected in the diesel fuel (CH- and CHOx-class) received roughly 100-fold higher signal intensities when using DMAN as a dopant. Furthermore, the number of detected compounds as well as the double bond equivalent of the detected compounds increased. The compound class distribution shifted when adding DMAN and the formerly dominant CHO2-, CHO3-, and CHO4- classes received similar relative intensities as formerly less accessible classes. The findings depict DMAN as a promising additive for electrospray ionisation negative analysis of at least mildly acidic compounds, even within complex sample material.

Comprehensive chemical comparison of fuel composition and aerosol particles emitted from a ship diesel engine by gas chromatography atmospheric pressure chemical ionisation ultra-high resolution mass spectrometry with improved data processing routines.

The analysis of petrochemical materials and particulate matter originating from combustion sources remains a challenging task for instrumental analytical techniques. A detailed chemical characterisation is essential for addressing health and environmental effects. Sophisticated instrumentation, such as mass spectrometry coupled with chromatographic separation, is capable of a comprehensive characterisation, but needs advanced data processing methods. In this study, we present an improved data processing routine for the mass chromatogram obtained from gas chromatography hyphenated to atmospheric pressure chemical ionisation and ultra high resolution mass spectrometry. The focus of the investigation was the primary combustion aerosol samples, i.e. particulate matter extracts, as well as the corresponding fossil fuels fed to the engine. We demonstrate that utilisation of the entire transient and chromatographic information results in advantages including minimisation of ionisation artefacts and a reliable peak assignment. A comprehensive comparison of the aerosol and the feed fuel was performed by applying intensity weighted average values, compound class distribution and principle component analysis. Certain differences between the aerosol generated with the two feed fuels, diesel fuel and heavy fuel oil, as well as between the aerosol and the feed were revealed. For the aerosol from heavy fuel oil, oxidised species from the CHN and CHS class precursors of the feed were predominant, whereas the CHOx class is predominant in the combustion aerosol from light fuel oil. Furthermore, the complexity of the aerosol increases significantly compared to the feed and incorporating a higher chemical space. Coupling of atmospheric pressure chemical ionisation to gas chromatography was found to be a useful additional approach for characterisation of a combustion aerosol, especially with an automated utilisation of the information from the ultra-high resolution mass spectrometer and the chromatographic separation.

Chemical Diversity and Complexity of Scotch Whisky as Revealed by High-Resolution Mass Spectrometry

Scotch Whisky is an important product, both culturally and economically. Chemically, Scotch Whisky is a complex mixture, which comprises thousands of compounds, the nature of which are largely unknown. Here, we present a thorough overview of the chemistry of Scotch Whisky as observed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Eighty-five whiskies, representing the majority of Scotch Whisky produced and sold, were analyzed by untargeted high-resolution mass spectrometry. Thousands of chemical formulae were assigned for each sample based on parts-per-billion mass accuracy of FT-ICR MS spectra. For the first time, isotopic fine structure analysis was used to confirm the assignment of high molecular weight CHOS species in Scotch Whisky. The assigned spectra were compared using a number of visualization techniques, including van Krevelen diagrams, double bond equivalence (DBE) plots, as well as heteroatomic compound class distributions. Additionally, multivariate analysis, including PCA and OPLS-DA, was used to interpret the data, with key compounds identified for discriminating between types of whisky (blend or malt) or maturation wood type. FT-ICR MS analysis of Scotch Whisky was shown to be of significant potential in further understanding of the complexity of mature spirit drinks and as a tool for investigating the chemistry of the maturation processes.Graphical ᅟ

Photochemical changes in water accommodated fractions of MC252 and surrogate oil created during solar exposure as determined by FT-ICR MS

To determine effects of photochemical weathering of petroleum, surrogate and Macondo (MC252) crude oils were exposed to solar radiation during the formation of Water Accommodated Fractions (WAFs) in sterile seawater. Samples were incubated in either unfiltered sunlight, with ultraviolet radiation blocked (Photosynthetically Active Radiation [PAR] only), or in darkness. WAFs were collected at two time points over the course of a week. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) analyses of water soluble species formed during exposure to sunlight were compared for the different treatments. Photochemical alterations resulted in differences in compound class distributions. In general, surrogate oil was photo-oxidized across a wider carbon number range compared to MC252. While photochemical differences were observed between MC252 and surrogate oils, microbial production in seawater responded similarly to both WAFs from both types of oils with the majority of the inhibition resulting from oil exposure to visible light.

Detection of residual oil-sand-derived organic material in developing soils of reclamation sites by ultra-high-resolution mass spectrometry.

The reconstruction of disturbed landscapes back to working ecosystems is an issue of increasing importance for the oil sand areas in Alberta, Canada. In this context, the fate of oil-sand-derived organic material in the tailings sands used for reclamation is of utmost environmental importance. Here we use electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry of maltene fractions to identify compositional variations over a complete oil sand mining and recultivation process chain. On the basis of bulk compound class distributions and percentages of unique elemental compositions, we identify specific compositional features that are related to the different steps of the process chain. The double bond equivalent and carbon number distributions of the N1 and S1O2 classes are almost invariant along the process chain, despite a significant decrease in overall abundance. We thus suggest that these oil-sand-derived components can be used as sensitive tracers of residual bitumen, even in soils from relatively old reclamation sites. The patterns of the O2, O3, and O4 classes may be applied to assess process-chain-related changes in organic matter composition, including the formation of plant-derived soil organic matter on the reclamation sites. The N1O2 species appear to be related to unidentified processes in the tailings ponds but do not represent products of aerobic biodegradation of pyrrolic nitrogen compounds.

Maturity-Driven Generation and Transformation of Acidic Compounds in the Organic-Rich Posidonia Shale as Revealed by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

The Posidonia Shale in the Hils syncline in North-West Germany represents a natural maturity sequence from 0.48 to 1.45% vitrinite reflectance (R0). In this study, the molecular composition of the acidic compounds of six Posidonia Shale samples with a different maturation level has been determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with electrospray ionization (ESI) in the negative ion mode. The changes in the distribution of elemental and compound classes as well as of double-bond equivalents (DBE) and carbon numbers at the different maturity levels are described in detail. Aromatic N1, N1O1, and N1S1 compounds are preferably formed during ongoing maturation, while the amount of O2 compounds decreases. With increasing thermal stress, condensation and aromatization of the acidic NSO compounds increases. In the sample of highest maturity (R0 1.45%), which has been shown to have a relevant shale gas potential, a significant enrichment of nonalkylated and methylated highly aromatic N1, N1O1, and N1S1 compounds has been observed, which can be the result of thermally induced side chain cracking of compounds with a higher alkylation degree. The other cracking products would be short chain hydrocarbons contributing to a significant amount to the overall gas potential of the Posidonia Shale.

Effects of experimental conditions on the molecular composition of maltenes and asphaltenes derived from oilsands bitumen: Characterized by negative-ion ESI FT-ICR MS

A vacuum topped Canadian oilsands bitumen (VTB) was subjected to solvent precipitation and subsequently characterized by elemental analysis, gel permeation chromatograph (GPC), 1H-NMR spectroscopy and negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Effects of experimental conditions such as solvent types (n-C5, n-C6, and n-C7), solvent purity, and solvent washing time on asphaltenes yields, bulk composition, and molecular composition of detectable heteroatom compounds in ESI source were determined. Elemental nitrogen and sulfur were enriched in asphaltenes while elemental oxygen had comparable content in maltenes and asphaltenes. Molecular composition of asphaltenes varies with separation conditions. The N1 and O1 species identified by ESI FT-ICR MS were enriched in maltenes. The O2 species exhibited two different double bond equivalents (DBE) distributions and solubility in normal paraffin solvents, indicating two types of molecular structures. Multi oxygen atom containing compounds mainly detected in asphaltenes. Compound class distributions are similar for maltenes derived from n-C5, n-C6, and n-C7, as well as for asphaltenes. The cyclic paraffin impurities in normal paraffin solvents had a significant influence on asphaltenes yields and heteroatom molecular composition. A portion of neutral N1 species and acidic O2 species adsorbed on asphaltenes could be dissolved by increasing washing time. Cautions should be exercised when interpreting the properties and composition of asphaltenes obtained with different experimental conditions.

Characterization of Saturates, Aromatics, Resins, and Asphaltenes Heavy Crude Oil Fractions by Atmospheric Pressure Laser Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

In this study, a heavy crude oil sample was separated on the basis of solubility and polarity, resulting in saturates, aromatics, resins, and asphaltenes (SARA) fractions. The fractions were analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled to atmospheric pressure laser ionization (APLI). On the basis of the APLI–FT-ICR MS results, the molecular formulas and their corresponding aromaticity were compared to the bulk crude oil. The maltenes showed almost identical compound class distribution to the bulk sample, while the subfractions of the maltenes denoted unique distributions in compound classes and aromaticity. The aromaticity distributions of the fractions were in good agreement with expectations; however, the resins fraction showed higher aromaticity than the aromatics fraction. The potential of the SARA fractionation method as a sample-simplification tool that allows for a reduction of components present during the measurements was also demonstrated using APLI...

Distribution of acids and nitrogen-containing compounds in biodegraded oils of the Liaohe Basin by negative ion ESI FT-ICR MS

Seven reservoir core (tar sand) bitumens of identical source and similar maturity from the Liaohe Basin of northeast China possess a natural sequence of increasing severity of biodegradation. This set of samples provides us an opportunity to study the change in oil composition or compound class distributions with biodegradation severity by negative ion electrospray Fourier transform-ion cyclotron resonance mass spectrometry (FT ICR-MS). The bitumen extracts from two columns (Es3 and Es1) were separated into maltene and asphaltene fractions for analysis of heteroatomic species by ESI FT-ICR MS. The maltene fractions were found to mainly contain N1, N1O1, N1O2, N1O3, O1, O2, O3 and O4 classes, while the asphaltene fractions mainly contain N1, N2O1, N1O1, N1O2, N1O3, N1O4, O2, O3, O4 and O5 classes. These species identified by FT-ICR MS in asphaltene fractions are likely to be chemisorbed/coprecipitated compounds, or the species precipitated due to high polarity during deasphaltene process. The susceptibility of compound classes and homologous series to biodegradation was studied based on the relative abundances. The results indicate that microorganisms alter the distribution of acids and nitrogen-containing compounds by selective removal and preservation of certain classes of compounds according to their susceptibility to biodegradation. For example, O2 and N1O2 classes increase significantly while N1 and N1O1 classes decrease with biodegradation. The differences in the susceptibility to microbial alteration within acyclic acids, 4–5 ring acids and 1–2 ring acids are discussed and the differences in the susceptibility of homologous series of heteroatom-containing polycyclic aromatic hydrocarbons are also discussed in this work.

Molecular Characterization and Comparison of Shale Oils Generated by Different Pyrolysis Methods

Shale oils generated using different laboratory pyrolysis methods have been studied using standard oil characterization methods as well as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI) and atmospheric photoionization (APPI) to assess differences in molecular composition. The pyrolysis oils were generated from samples of the Mahogany zone oil shale of the Eocene Green River Formation collected from outcrops in the Piceance Basin, Colorado, using three pyrolysis systems under conditions relevant to surface and in situ retorting approaches. Significant variations were observed in the shale oils, particularly the degree of conjugation of the constituent molecules and the distribution of nitrogen-containing compound classes. Comparison of FT-ICR MS results to other oil characteristics, such as specific gravity; saturate, aromatic, resin, asphaltene (SARA) distribution; and carbon number distribution determined by gas chromatography, indicated correspondence between higher average double bond equivalence (DBE) values and increasing asphaltene content. The results show that, based on the shale oil DBE distributions, highly conjugated species are enriched in samples produced under low pressure, high temperature conditions, and under high pressure, moderate temperature conditions in the presence of water. We also report, for the first time in any petroleum-like substance, the presence of N4 class compounds based on FT-ICR MS data. Using double bond equivalence and carbon number distributions, structures for the N4 class and other nitrogen-containing compounds are proposed.

Distribution, degradation and dynamics of dissolved organic carbon and its major compound classes in the Pearl River estuary, China

We investigated the distribution, degradation and dynamics of organic carbon and its major compound classes, carbohydrates and amino acids, based upon a cruise in the Pearl River estuary in April 2007. Dissolved oxygen (DO), nutrients, particulate organic carbon (POC), chlorophyll a (Chl a), dissolved organic carbon (DOC), total dissolved carbohydrates (TCHO, including monosaccharides, MCHO, and polysaccharides, PCHO) as well as total dissolved amino acids (TAA, both dissolved free, DFAA, and combined components, DCAA) were measured along a salinity gradient. Community respiration and biodegradable DOC were also determined via both short term (within 3 days) and long term (lasting 30 days) incubation. DOC, MCHO, TCHO, DFAA and TAA concentrations were high in the upper reach of the Pearl River estuary and decreased rapidly downstream. Anthropogenic sewage input appeared to be an important source of the DOC pool in the upper estuary. DOC distribution was non-conservative during the estuarine mixing, showing a net consumption of DOC in the upper reach and in the low salinity ( S < 20) region of the Pearl River estuary. Changes in the relative compositions of carbohydrates (MCHO vs. PCHO) and amino acids (DFAA vs. DCAA) along the salinity gradient further indicated that different processes (biodegradation, flocculation, and phytoplankton production) had different influences on distributions of organic compound classes in this estuarine system. Our one-month incubation experiment further revealed that a substantial portion (15–45%) of DOC from the estuary was biodegradable. Bacterial respiration rates were much higher (0.12–5.8 μmol O 2 L − 1 h − 1 ) than the DOC consumption rates, suggesting that there were other oxygen consumption processes, such as nitrification besides the aerobic respiration of organic matter in the Pearl River estuary, as inferred by the distribution of NH 4 + and NO 3 −. We estimated that 5.3 × 10 8 g C d − 1 of DOC can be exported out from the Lingdingyang Bay (a major subestuary of the Pearl River estuary) to the continental shelf of the South China Sea during this low flow season.

Composition of organic matter in particle size fractionated pig slurry

Pig slurry is a heterogeneous mixture of different particle sizes that will have different mobility in soil. Therefore, a physically fractionated pig slurry sample was analysed, e.g. using pyrolysis-field ionisation mass spectrometry (Py-FIMS) in an effort to identify relationships between particle size and composition of organic matter. The presumably most mobile fractions in soils (<63 μm) accounted for ≈50% of slurry dry matter and were dominated by lignins, and N-containing compounds. Sterols were especially abundant in the larger-sized fractions, which corresponds to their reported distribution in soils and surface waters. The averaged molecular masses indicated similarities of fractions <10 μm to aquatic humic substances and increasing content of plant material with increasing particle size. A statistical analysis of the compound class distribution revealed that the analysis of three particle size fractions is essential for the assessment of the composition and properties of slurry constituents.