High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems

In vivo comprehensive multiphase NMR

Traditionally, due to different hardware requirements, nuclear magnetic resonance (NMR) has developed as two separate fields: one dealing with solids, and one with solutions. Comprehensive multiphase (CMP) NMR combines all electronics and hardware (magic angle spinning [MAS], gradients, high power Radio Frequency (RF) handling, lock, susceptibility matching) into a universal probe that permits a comprehensive study of all phases (i.e., liquid, gel-like, semisolid, and solid), in intact samples. When applied in vivo, it provides unique insight into the wide array of bonds in a living system from the most mobile liquids (blood, fluids) through gels (muscle, tissues) to the most rigid (exoskeleton, shell). In this tutorial, the practical aspects of in vivo CMP NMR are discussed including: handling the organisms, rotor preparation, sample spinning, water suppression, editing experiments, and finishes with a brief look at the potential of other heteronuclei (² H, ¹⁵ N, ¹⁹ F, ³¹ P) for in vivo research. The tutorial is aimed as a general resource for researchers interested in developing and applying MAS-based approaches to living organisms. Although the focus here is CMP NMR, many of the approaches can be adapted (or directly applied) using conventional high-resolution magic angle spinning, and in some cases, even standard solid-state NMR probes.

Optical Properties of Soil Dissolved Organic Matter Are Related to Acidic Functions of Its Components as Revealed by Fractionation, Selective Deuteromethylation, and Ultrahigh Resolution Mass Spectrometry

The goal of this study was to establish a relationship between the optical properties of soil dissolved organic matter (DOM) and acidic functions carried out by its individual constituents. We obtained 12 fractions of DOM samples using sequential solid phase extraction on nonionic sorbent at steadily lowered pH values: 7, 5, 3, 2, which correspond to low bounds of pK_a values of phenols, aliphatic, and aromatic carboxylic acids, and ketoacids. The structural studies were conducted with the use of NMR and selective deuteromethylation of isolated fractions coupled to ultrahigh resolution mass spectrometry. First, a gradual shift of molecular compositions was observed from reduced components to aromatic oxidized compounds isolated at pH 7 and 2, respectively. Changes in molecular compositions were accompanied by a red shift of fluorescence spectra. Further application of deuteromethylation enabled us to distinguish DOM constituents with different amounts of carboxylic groups. Moreover, identification of structural isomers in a single DOM sample was achieved. Statistical analysis revealed that red shift of fluorescence is facilitated by the increase of a contribution of aromatic poly(carboxylic acid)s with high conjugation lengths. Additionally, analysis of the labeled fractionated permafrost thaw DOM directly showed carboxyl-rich alicyclic molecules, while the same components from lower-latitude DOM were assigned to lignin-like species.

Molecular differences between water column and sediment pore water SPE-DOM in ten Swedish boreal lakes

Boreal lakes are considered hot spots of dissolved organic matter (DOM) processing within the global carbon cycle. This study has used FT-ICR mass spectrometry and comprehensive data evaluation to assess the molecular differences of SPE-DOM between lake column water SPE-DOM and sedimentary pore water SPE-DOM in 10 Swedish boreal lakes of the Malingsbo area, which were selected for their large diversity of physicochemical and morphological characteristics. While lake column water is well mixed and fairly oxygenated, sedimentary pore water is subject to depletion of oxygen and to confinement of molecules. Robust trends were deduced from molecular compositions present in all compartments and in all 10 lakes ("common compositions") with recognition of relative abundance. Sedimentary pore water SPE-DOM featured higher proportions of heteroatoms N and S, higher average H/C ratios in presence of higher DBE/C ratios, and higher average oxygenation than lake column water SPE-DOM. These trends were observed in all lakes except Ljustjärn, which is a ground water fed kettle lake with an unique lake biogeochemistry. Analogous trends were also observed in case of single or a few lakes and operated also for compounds present solely in either lake column water or sedimentary pore water. Unique compounds detected in either compartments and/or in a few lakes showed higher molecular diversity than the "common compositions". Processing of DOM molecules in sediments included selective preservation for polyphenolic compounds and microbial resynthesis of selected molecules of considerable diversity.

Reading From the Crystal Ball: The Laws of Moore and Kurzweil Applied to Mass Spectrometry in Food Analysis

Predictions about the future knowledge of the “complete” food metabolome may be assayed based on the laws of Moore and Kurzweil, who foresee a technological development on exponential behavior. The application of these laws allows us to extrapolate and predict roughly when each single metabolite in foods could be (1) known, (2) detectable, and (3) identifiable. To avoid huge additional uncertainties, we restrict the range of metabolites to those in unprocessed foods. From current metabolite databases and their coverage over time, the conservative number of all considered food metabolites can be estimated to be 500,000, predicting them being known by around 2025. Assuming these laws and extrapolating the current developments in chromatography and mass spectrometry technology, the year 2032 can be estimated, when single molecule detection will be possible in “routine” mass spectrometry. A possible forecast for the identification of all food metabolites, however, is much more difficult and estimated at the earliest in 2041 as the year when this may be achieved. However, the real prediction uncertainty is extreme and is discussed in the essay presented here.

Mathematical chromatography deciphers the molecular fingerprints of dissolved organic matter

Mathematical chromatography offers information reduction and feature extraction in complex liquid chromatography—mass spectrometry datasets.

NMR assignment of the in vivo daphnia magna metabolome

Daphnia (freshwater fleas) are among the most widely used organisms in regulatory aquatic toxicology/ecology, while their recent listing as an NIH model organism is stimulating research for understanding human diseases and processes.

Molecular Composition of Size-Fractionated Fulvic Acid-Like Substances Extracted from Spent Cooking Liquor and Its Relationship with Biological Activity

The treatment of spent cooking liquor is critical for clean production of pulp and paper industry. There is a compelling need to develop a cost-effective and green technology for reuse of organic matter in spent cooking liquor to mitigate the negative impacts on the environment. The objective of this study is to examine the chemical structure of fulvic acid-like substances extracted from spent cooking liquor (PFA) and their relationship with bioactivity in plant growth. Compared with the benchmark Pahokee peat fulvic acid (PPFA), PFA has less aromatic structure, but higher content of lignin, carbohydrates, and amino acid. After fractionation, protein/amino proportion decreased with increasing molecular weight, but the aromaticity increased. Under salt stress, rice seedling growth was promoted by PFA with low molecular weight (<5 kDa), but inhibited by fraction with high molecular weight (>10 kDa). Principal component analysis suggested that promoted growth was more related with chemical structure (O- and N-alkyl moieties) than with molecular weight. This study provided the theoretical basis for development of an innovative green technology of sustainable reuse of spent cooking liquor in agriculture.

Molecular change of dissolved organic matter and patterns of bacterial activity in a stream along a land-use gradient

Fluvial networks are globally relevant for the processing of dissolved organic matter (DOM). To investigate the change in molecular DOM diversity along the river course, high-field FTICR mass spectrometry and NMR spectroscopy of riverine DOM as well as bacterial abundance and activity were measured in a third order stream along a land-use gradient from pristine, agricultural to urban landscapes. DOM composition showed a clear evolution along the river course with an initial decrease of average oxidation and unsaturation followed by an increased relative abundance of CHNO and CHOS compounds introduced by agriculture and waste water, respectively. DOM composition was dominated by rather unsaturated CHO compounds (H/C ≤ 1) in headwaters and by more aliphatic molecules at downstream sites. Oxygenated functional groups shifted from aromatic ethers and hydroxyl groups to aliphatic carboxylic acids and aliphatic hydroxyl groups. This massive dislocation of oxygen significantly increased the diversity of atomic environments in branched aliphatic groups from headwater to downstream DOM. Mass spectra of DOM enabled the detection of compositional relationships to bacterial abundance and activity which was positively related to more aliphatic components (H/C > 1) and negatively related to unsaturated components. FTICR mass and NMR spectra corroborated the initial decline in DOM molecular diversity predicted by the River Continuum Concept (RCC) but demonstrated an anthropogenic increase in the molecular diversity of DOM further downstream. While the high DOM molecular diversity in first order headwater streams was the result of small scale ecosystem plurality, agriculture and waste water treatment introduced many components in the lower reaches. These anthropogenic influences together with massive bacterial oxidation of DOM contributed to a growth of molecular diversity of downstream DOM whose composition and structure differed entirely from those found in pristine headwaters.

Redox properties and dechlorination capacities of landfill-derived humic-like acids

Electron transfer capacities (ETC) of humic-like acids (HLA) and their effects on dechlorination are dependent on their redox-active properties. Aging and minerals can affect the chemical compositions and structures of HLA. However, the underlying mechanism and the impacts on the dechlorination capacities of HLA are poorly understood. We investigated how redox properties change in association with the intrinsic chemical natures and exterior minerals of the HLA extracted from landfilled solid wastes. Furthermore, the ETC of the landfill-derived HLA could be strengthened by increasing landfill age and demineralization, thereby facilitating the dechlorination of pentachlorophenol (PCP). The HLA molecules started to polymerize aromatic macromolecules during landfilling, leading to an increase in ETC and dechlorination capacities. Macromolecular HLA were dissociated to smaller molecules and exposed more aromatic and carboxyl groups when separated from minerals, which enhanced the ETC and the dechlorination abilities of the HLA. Microbial-mediated dechlorination was an effective way to degrade PCP, and almost 80% of the PCP was transformed after 40 days of demineralized HLA and Shewanella oneidensis MR-1 incubation. The demineralization and aging further facilitated the microbial-mediated PCP dechlorination. The findings provide a scientific base for improving in-situ bioremediation of chlorinated compound-contaminated soils using freshly synthesized HLA.

Examination of molecular space and feasible structures of bioactive components of humic substances by FTICR MS data mining in ChEMBL database

Humic substances (HS) are complex natural mixtures comprising a large variety of compounds produced during decomposition of decaying biomass. The molecular composition of HS is extremely diverse as it was demonstrated with the use of high resolution mass spectrometry. The building blocks of HS are mostly represented by plant-derived biomolecules (lignins, lipids, tannins, carbohydrates, etc.). As a result, HS show a wide spectrum of biological activity. Despite that, HS remain a 'biological activity black-box' due to unknown structures of constituents responsible for the interaction with molecular targets. In this study, we investigated the antiviral activity of eight HS fractions isolated from peat and coal, as well as of two synthetic humic-like materials. We determined molecular compositions of the corresponding samples using ultra-high resolution Fourier-transform ion cyclotron resonance mass-spectrometry (FTICR MS). Inhibitory activity of HS was studied with respect to reproduction of tick-borne encephalitis virus (TBEV), which is a representative of Flavivirus genus, and to a panel of enteroviruses (EVs). The samples of natural HS inhibited TBEV reproduction already at a concentration of 1 µg/mL, but they did not inhibit reproduction of EVs. We found that the total relative intensity of FTICR MS formulae within elemental composition range commonly attributed to flavonoid-like structures is correlating with the activity of the samples. In order to surmise on possible active structural components of HS, we mined formulae within FTICR MS assignments in the ChEMBL database. Out of 6502 formulae within FTICR MS assignments, 3852 were found in ChEMBL. There were more than 71 thousand compounds related to these formulae in ChEMBL. To support chemical relevance of these compounds to natural HS we applied the previously developed approach of selective isotopic exchange coupled to FTICR MS to obtain structural information on the individual components of HS. This enabled to propose compounds from ChEMBL, which corroborated the labeling data. The obtained results provide the first insight onto the possible structures, which comprise antiviral components of HS and, respectively, can be used for further disclosure of antiviral activity mechanism of HS.

Structural investigation of coal humic substances by selective isotopic exchange and high-resolution mass spectrometry

Here, we report the application of a selective liquid-phase hydrogen/deuterium exchange (HDX) coupled to ultra-high resolution FTICR MS for structural investigations of individual constituents of humic substances (HS) isolated from three coal samples of different geographical origin. Selectivity was achieved by conducting reactions in DCl or NaOD solutions for catalyzing HDX in aromatic ring and side-chain positions with enhanced C-H acidity, respectively. FTICR MS analysis showed a significant overlap of molecular compositions in the HS samples under study, with 2000 common formulae. Using HDX, we demonstrated that the determined common formulae are presented by different structural isomers. We found that aromatic compounds varied both in the substitution pattern and the number of aromatic protons. Depending on the sample, lignin components with the same molecular formulae were composed of coumaryl, coniferyl or sinapyl moieties. Enumeration of HDX series for the 800 most abundant compounds showed that the results of HDX agreed well with the model structures suggested for humic components occupying a van Krevelen plot. In addition, we explored chemical transformations, which could connect individual constituents of coal HS. These transformations included hydrolysis of a guaiacyl moiety and reduction of a catechol unit, which corresponds to the conversion of a coniferyl fragment into a coumaryl unit. The obtained results were supportive of the hypothesis of the reducing humification pathway suggested for lignin transformation in the environment. The conclusion was made that the molecular ensemble of coal HS is composed of individual constituents produced at different humification stages.

Pushing the analytical limits: new insights into complex mixtures using mass spectra segments of constant ultrahigh resolving power

A new strategy has been developed for characterization of the most challenging complex mixtures to date, using a combination of custom-designed experiments and a new data pre-processing algorithm. In contrast to traditional methods, the approach enables operation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with constant ultrahigh resolution at hitherto inaccessible levels (approximately 3 million FWHM, independent of m/z). The approach, referred to as OCULAR, makes it possible to analyze samples that were previously too complex, even for high field FT-ICR MS instrumentation. Previous FT-ICR MS studies have typically spanned a broad mass range with decreasing resolving power (inversely proportional to m/z) or have used a single, very narrow m/z range to produce data of enhanced resolving power; both methods are of limited effectiveness for complex mixtures spanning a broad mass range, however. To illustrate the enhanced performance due to OCULAR, we show how a record number of unique molecular formulae (244 779 elemental compositions) can be assigned in a single, non-distillable petroleum fraction without the aid of chromatography or dissociation (MS/MS) experiments. The method is equally applicable to other areas of research, can be used with both high field and low field FT-ICR MS instruments to enhance their performance, and represents a step-change in the ability to analyze highly complex samples.

From green chemistry and nature-like technologies towards ecoadaptive chemistry and technology

Nature-like technologies can be considered as a logical development of green chemistry principles implemented to design novel materials and processes aimed at mimicking and reproducing natural life-sustaining mechanisms on molecular level. Humic substances which penetrate throughout the entire environment and represent from 50 to 90% of organic matter in soil and water ecosystems, play multiple life-sustaining functions on Earth. To name a few, HS regulate transport and availability of biogenic elements to plants, immobilize and mitigate toxicity of hazardous elements in the contaminated ecosystems, protect plants from non-specific abiotic stresses, play key role for fertility of soils determining water-retention and structure. Here we represent a novel platform for nature-inspired synthesis of soft and hybrid (nano)materials aimed at their use for soil and water clean up, carbon sequestration, soil fertility restoration. It is based on a smart use of natural hyperbranched polyelectrolytes – humic substances, which possess multiple functional groups including carboxyl, hydroxyl, amide, and others. Multiple functional groups of HS make them amenable both for classical chemical modification as well as for producing interpolyelectrolyte complexes. In this work, we present both approaches for manufacturing silicon-containing humic derivatives and supramolecular complexes with acquired new property – self-adhesion to both inorganic and bio-surfaces. The synthesis is conducted using humic materials from different sources and functional organosilanes. Self-assembly of the supramolecular silicon-humic systems occurs with formation of humic-silsesquioxane networks capable to adhere to mineral surfaces. This process is similar to immobilization of organic coatings to mineral surfaces. We have shown how this process can be realized in the ground waters for the purposes of the environmental clean up. We have also proposed to use the silicon-humic complexes for improving humus content of soils and for reconstructing soil restoration processes both in the lab and in the field. Another field of our research is synthesis of iron-containing humics-stabilized nanoparticles (NPs), which can be used as a source for plants nutrition instead of synthetic iron chelates. The idea is based on the natural phenomenon that in soils, water-stable sols of iron-containing NPs are formed due to complexing with HS, which can bind large amounts of poorly ordered iron (hydr)oxides providing for stabilization of colloidal iron in the form of NPs. It has been numerously shown that the presence of HS improves iron acquisition by plants in soils, but there was no systematic study so far with respect to a relationship between size and crystallinity of humics-stabilized iron-containing NPs and their availability to plants. We have conducted such a study and could establish conditions when humics-stabilized NPs could be taken up by plants with similar efficiency as FeEDTA. The presented data demonstrate good prospects for a use of green humics-based materials in nature-like technologies. We also hope that these studies will give rise to new branch of chemistry and technology which can be called ecoadaptive chemistry and technology.

Assessing the potential of quantitative 2D HSQC NMR in 13C enriched living organisms

In vivo Nuclear Magnetic Resonance (NMR) spectroscopy has great potential to interpret the biochemical response of organisms to their environment, thus making it an essential tool in understanding toxic mechanisms. However, magnetic susceptibility distortions lead to 1D NMR spectra of living organisms with lines that are too broad to identify and quantify metabolites, necessitating the use of 2D ¹H-¹³C Heteronuclear Single Quantum Coherence (HSQC) as a primary tool. While quantitative 2D HSQC is well established, to our knowledge it has yet to be applied in vivo. This study represents a simple pilot study that compares two of the most popular quantitative 2D HSQC approaches to determine if quantitative results can be directly obtained in vivo in isotopically enriched Daphnia magna (water flea). The results show the perfect-HSQC experiment performs very well in vivo, but the decoupling scheme used is critical for accurate quantitation. An improved decoupling approach derived using optimal control theory is presented here that improves the accuracy of metabolite concentrations that can be extracted in vivo down to micromolar concentrations. When combined with 2D Electronic Reference To access In vivo Concentrations (ERETIC) protocols, the protocol allows for the direct extraction of in vivo metabolite concentrations without the use of internal standards that can be detrimental to living organisms. Extracting absolute metabolic concentrations in vivo is an important first step and should, for example, be important for the parameterization as well as the validation of metabolic flux models in the future.

1D "Spikelet" Projections from Heteronuclear 2D NMR Data-Permitting 1D Chemometrics While Preserving 2D Dispersion

Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the non-targeted metabolomics of intact biofluids and even living organisms. However, spectral overlap can limit the information that can be obtained from 1D 1H NMR. For example, magnetic susceptibility broadening in living organisms prevents any metabolic information being extracted from solution-state 1D 1H NMR. Conversely, the additional spectral dispersion afforded by 2D 1H-13C NMR allows a wide range of metabolites to be assigned in-vivo in 13C enriched organisms, as well as a greater depth of information for biofluids in general. As such, 2D 1H-13C NMR is becoming more and more popular for routine metabolic screening of very complex samples. Despite this, there are only a very limited number of statistical software packages that can handle 2D NMR datasets for chemometric analysis. In comparison, a wide range of commercial and free tools are available for analysis of 1D NMR datasets. Overtime, it is likely more software solutions will evolve that can handle 2D NMR directly. In the meantime, this application note offers a simple alternative solution that converts 2D 1H-13C Heteronuclear Single Quantum Correlation (HSQC) data into a 1D “spikelet” format that preserves not only the 2D spectral information, but also the 2D dispersion. The approach allows 2D NMR data to be converted into a standard 1D Bruker format that can be read by software packages that can only handle 1D NMR data. This application note uses data from Daphnia magna (water fleas) in-vivo to demonstrate how to generate and interpret the converted 1D spikelet data from 2D datasets, including the code to perform the conversion on Bruker spectrometers.

Systems chemical analytics: introduction to the challenges of chemical complexity analysis

We present concepts of complexity, and complex chemistry in systems subjected to biotic and abiotic transformations, and introduce analytical possibilities to disentangle chemical complexity into its elementary parts as a global integrated approach termed systems chemical analytics.

Metabolic Profiling Using In Vivo High Field Flow NMR

In vivo NMR (nuclear magnetic resonance) has the potential to monitor and record metabolic flux in close to real time, which is essential for better understanding the toxic mode of action of a contaminant and deciphering complex interconnected stress-induced pathways impacted inside an organism. Here, we describe how to construct and use a simple flow system to keep small aquatic organisms alive inside the NMR spectrometer. In living organisms, magnetic susceptibility distortions lead to severe broadening in conventional NMR. Two main approaches can be employed to overcome this issue: (1) use a pulse sequence to reduce the distortions, or (2) employ multidimensional NMR in combination with isotopic enrichment to provide the spectral dispersion required to separate peaks from overlapping resonances. Both approaches are discussed, and protocols for both approaches are provided here in the context of small aquatic organisms.

Focusing on “the important” through targeted NMR experiments: an example of selective13C–12C bond detection in complex mixtures

Here, a targeted NMR experiment is introduced which selectively detects the formation of¹³C–¹²C bonds in mixtures.

Microbiome-Triggered Transformations of Trace Organic Chemicals in the Presence of Effluent Organic Matter in Managed Aquifer Recharge (MAR) Systems

It is widely assumed that biodegradation of trace organic chemicals (TOrCs) in managed aquifer recharge (MAR) systems occurs via a cometabolic transformation with dissolved organic carbon serving as primary substrate. Hence, the composition facilitating bioavailability of the organic matter seems to have a great impact on TOrCs transformation in MAR systems. The aim of this study was to elucidate the character of effluent organic matter present in the feedwater of a simulated sequential MAR system throughout the infiltration by use of FT-ICR-MS analyses as well as spectroscopic methods. Furthermore, compositional changes were correlated with TOrCs targeted throughout the system as well as the abundance of different microbial phyla. On the basis of their behavior throughout the infiltration system in which different redox and substrate conditions prevailed, TOrCs were classified in four groups: easily degradable, redox insensitive, redox sensitive, and persistent. Masses correlating with persistent TOrCs were mainly comprised of CHNO-containing molecules but also of CHO which are known as carboxyl-rich alicyclic molecules, while CHOS and CHNOS can be neglected. Easily degradable TOrCs could be associated with CHNO-, CHO-, and CHOS-containing compounds. However, a shift of molecular compounds to mostly CHOS was observed for redox-insensitive TOrCs. Three hundred thirty eight masses correlated with removal of redox-sensitive TOrCs, but no distinct clustering was identified.

Separation of Benzoic and Unconjugated Acidic Components of Leonardite Humic Material Using Sequential Solid-Phase Extraction at Different pH Values as Revealed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Correlation Nuclear Magnetic Resonance Spectroscopy

Here, we report on sequential solid-phase extraction of leonardite hymatomelanic acid (CHM) on a non-ionic sorbent at four steadily lowered pH values: 7, 5, 3, and 2, yielding fractions with different acidic properties. Using nuclear magnetic resonance (NMR) spectroscopy and ultrahigh-resolution mass spectrometry, we revealed a gradual shift of dominating scaffolds in the fractions of CHM from reduced saturated to oxidized aromatic compounds. An increase on the average aromaticity of the CHM fractions was accompanied by a red shift in fluorescence spectra. These results were supported by heteronuclear single quantum coherence and heteronuclear multiple bond correlation NMR experiments. We have demonstrated that the CHM fraction isolated at pH 5 was dominated by aliphatic carboxyl carriers, while the pH 3 fraction was dominated by aromatic carboxyl acids. The developed fractionation technique will enable deeper insight on structure-property relationships and the design of the humic-based materials with tailored reactive properties.

Yellowstone Hot Springs are Organic Chemodiversity Hot Spots

Yellowstone National Park hydrothermal springs were investigated according to their organic geochemistry with a special focus on the Yellowstone hot spring dissolved organic matter (YDOM) that was solid-phase extracted. Here we show that YDOM has a unique chemodiversity that has not yet been observed anywhere else in aquatic surface environments and that Yellowstone hot springs are organic chemodiversity hot spots. Four main geochemically classified hot spring types (alkaline-chloride, mixed alkaline-chloride, acid-chloride-sulfate and travertine-precipitating) exhibited distinct organic molecular signatures that correlated remarkably well with the known inorganic geochemistry and manifested themselves in excitation emission matrix fluorescence, nuclear magnetic resonance, and ultrahigh resolution mass spectra. YDOM contained thousands of molecular formulas unique to Yellowstone of which 80% contained sulfur, even in low hydrogen sulfide containing alkaline-chloride springs. This unique YDOM reflects the extreme organic geochemistry present in the hydrothermal features of Yellowstone National Park.

Molecular Structure Characterization of Riverine and Coastal Dissolved Organic Matter with Ion Mobility Quadrupole Time-of-Flight LCMS (IM Q-TOF LCMS)

Deciphering molecular structures of dissolved organic matter (DOM) components is key to understanding the formation and transformation of this globally important carbon pool in aquatic environments. Such a task depends on the integrated use of complementary analytical techniques. We characterize the molecular structure of natural DOM using an ion mobility quadrupole time of flight liquid chromatography mass spectrometer (IM Q-TOF LC/MS), which provides multidimensional structural information on DOM molecules. Geometric conformation of DOM molecules is introduced into molecular-level analysis via the ion mobility (IM) in the system, and an actual measurement of isomers is achieved for the first time. Our data show that natural DOM molecules from several south Texas rivers and adjacent coastal waters have smaller geometric conformation compared with standard biomolecules. Furthermore, about 10% of all DOM molecules resolved within the detection limit of IM-MS had at least one but no more than four isomers. With acquired geometric and isomeric information, we established a multidimensional database containing 89 natural DOM compounds. This database provides a foundation to expand further, or compare, with DOM data from different seasons and locations.

In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity

Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.

Online HPLC-ESI-HRMS Method for the Analysis and Comparison of Different Dissolved Organic Matter Samples

Natural dissolved organic matter (DOM) is an ultracomplex mixture that is essential to global carbon cycling but is poorly understood because of its complexity. The most powerful tool for the DOM characterization is high-resolution mass spectrometry (HRMS) generally combined to direct infusion (DI) as sample introduction. Liquid chromatography (LC) represents a compelling alternative to DI; however, state-of-the-art techniques involve only offline LC-HRMS approaches, which have important logistical drawbacks that make DOM analysis more challenging. This study introduces a new method based on online coupling of liquid chromatography to high resolution mass spectrometry, able to overcome the disadvantages of usual approaches. It is characterized by high reproducibility (% Bray-Curtis dissimilarity among replicates ≈ 2.5%), and it reduces transient complexity and contaminant interferences, thus increasing the signal-to-noise ratio (S/N), leading to the identification of an overall larger number of formulas in the mixture. Moreover, the application of an in silico fractionation prior to the statistical analysis allows an easy, flexible, fast, and detailed comparison of DOM samples from a variety of sources with a single chromatographic run.

Extensive processing of sediment pore water dissolved organic matter during anoxic incubation as observed by high-field mass spectrometry (FTICR-MS)

Dissolved organic matter (DOM) contained in lake sediments is a carbon source for many microbial degradation processes, including aerobic and anaerobic mineralization. During anaerobic degradation, DOM is partially consumed and transformed into new molecules while the greenhouse gases methane (CH₄) and carbon dioxide (CO₂) are produced. In this study, we used ultrahigh resolution mass spectrometry to trace differences in the composition of solid-phase extractable (PPL resin) pore water DOM (SPE-DOM) isolated from surface sediments of three boreal lakes before and after 40 days of anoxic incubation, with concomitant determination of CH₄ and CO₂ evolution. CH₄ and CO₂ production detected by gas chromatography varied considerably among replicates and accounted for fractions of ∼2-4 × 10^-4 of sedimentary organic carbon for CO₂ and ∼0.8-2.4 × 10^-5 for CH₄. In contrast, the relative changes of key bulk parameters during incubation, such as relative proportions of molecular series, elemental ratios, average mass and unsaturation, were regularly in the percent range (1-3% for compounds decreasing and 4-10% for compounds increasing), i.e. several orders of magnitude higher than mineralization alone. Computation of the average carbon oxidation state in CHO molecules of lake pore water DOM revealed rather non-selective large scale transformations of organic matter during incubation, with depletion of highly oxidized and highly reduced CHO molecules, and formation of rather non-labile fulvic acid type molecules. In general, proportions of CHO compounds slightly decreased. Nearly saturated CHO and CHOS lipid-like substances declined during incubation: these rather commonplace molecules were less specific indicators of lake sediment alteration than the particular compounds, such as certain oxygenated aromatics and carboxyl-rich alicyclic acids (CRAM) found more abundant after incubation. There was a remarkable general increase in many CHNO compounds during incubation across all lakes. Differences in DOM transformation between lakes corresponded with lake size and water residence time. While in the small lake Svarttjärn, CRAM increased during incubation, lignin-and tannin-like compounds were enriched in the large lake Bisen, suggesting selective preservation of these rather non-labile aromatic compounds rather than recent synthesis. SPE-DOM after incubation may represent freshly synthesized compounds, leftover bulk DOM which is primarily composed of intrinsically refractory molecules and/or microbial metabolites which were not consumed in our experiments. In spite of a low fraction of the total DOM being mineralized to CO₂ and CH₄, the more pronounced change in molecular DOM composition during the incubation indicates that diagenetic modification of organic matter can be substantial compared to complete mineralization.

Environmental Nuclear Magnetic Resonance Spectroscopy: An Overview and a Primer

NMR spectroscopy is a versatile tool for the study of structure and interactions in environmental media such as air, soil, and water as well as monitoring the metabolic responses of living organisms to an ever changing environment. Part review, part perspective, and part tutorial, this Feature is aimed at nonspecialists who are interested in learning more about the potential and impact of NMR spectroscopy in environmental research.

Emergence of the Reactivity Continuum of Organic Matter from Kinetics of a Multitude of Individual Molecular Constituents

The reactivity continuum (RC) model is a powerful statistical approach for describing the apparent kinetics of bulk organic matter (OM) decomposition. Here, we used ultrahigh resolution mass spectrometry data to evaluate the main premise of the RC model, namely that there is a continuous spectrum of reactivity within bulk OM, where each individual reactive type undergoes exponential decay. We performed a 120 day OM decomposition experiment on lake water, with an untreated control and a treatment preexposed to UV light, and described the loss of bulk dissolved organic carbon with RC modeling. The behavior of individual molecular formulas was described by fitting the single exponential model to the change in peak intensities over time. The range of the empirically derived apparent exponential decay coefficients (k_exp) was indeed continuous. The character of the corresponding distribution, however, differed from the conceptual expectations, due to the effects of intrinsic averaging, overlaps in formula-specific loss and formation rates, and the limitation of the RC model to include apparently accumulating compounds in the analysis. Despite these limitations, both the RC model-simulated and empirical (mass spectrometry-derived) distributions of k_exp captured the effects of preexposure to UV light. Overall, we present experimental evidence that the reactivity continuum within bulk OM emerges from a range of reactivity of numerous individual components. This constitutes direct empirical support for the major assumption behind the RC model of the natural OM decomposition.

Mass spectrometry-based phytochemical screening for hypoglycemic activity of Fagioli di Sarconi beans (Phaseolus vulgaris L.)

The present study deals with the evaluation of antidiabetic activities of Fagioli di Sarconi beans (Phaseolus vulgaris), including 21 ecotypes protected by the European Union with the mark PGI (i.e., Protected Geographical Indication), and cultivated in Basilicata (southern Italy). For this purpose, α-glucosidase and α-amylase assays were assessed; among all bean ecotypes, the tight green seed colour of Verdolino extracts exhibited the highest α-glucosidase and α-amylase inhibitory activity with IC₅₀=1.1±0.1μg/ml and IC₅₀=19.3±1.1μg/ml, respectively. Phytochemical compound screening of all Fagioli di Sarconi beans performed by flow injection-electrospray ionization-ultrahigh resolution mass spectrometry (uHRMS) and based on the calculation of elemental formulas from accurate m/z values, was helpful to annotate specific compounds, such as alkaloids, saponins, flavonoids, and terpenoids, which are most likely responsible for their biological activity.

Analysis of DOM phototransformation using a looped NMR system integrated with a sunlight simulator

Photochemical transformation plays an important role in functionalizing and degrading dissolved organic matter (DOM), producing one of the most complex mixtures known. In this study, using a flow-based design, nuclear magnetic resonance (NMR) spectroscopy is directly interfaced with a sunlight simulator enabling the study of DOM photodegradation in situ with high temporal resolution over 5 days. Samples from Suwannee River (Florida), Nordic Reservoir (Norway), and Pony Lake (Antarctic) are studied. Phototransformation of DOM is dominated by the degradation of aromatics and unsaturated structures (many arising from lignin) into carboxylated and hydroxylated products. To assess longer term changes, the samples were continuously irradiated for 17.5 days, followed by the identification a wide range of compounds and assessment of their fate using off-line 2D-NMR. This study demonstrates the applicability of the looped system to follow degradation in a non-targeted fashion (the mixture as a whole) and target analysis (tracing specific metabolites), which holds great potential to study the fate and transformation of contaminants and nutrients in the presence of DOM. It also demonstrates that components that remain unresolved in 1D NMR can be identified using 2D methods.

Synthesis of carboxylated styrene polymer for internal calibration of Fourier transform ion cyclotron resonance mass-spectrometry of humic substances

We report synthesis and application of the novel carboxylated styrene for internal calibration of Fourier transform ion cyclotron resonance mass-spectra of humic substances. The calibrant was synthesized in five steps from acetylsalicylic acid (aspirin) followed by spontaneous polymerization of vinyl salicylic acid. Aromatic nature of the prepared polymer enabled its simultaneous analysis in the presence of the Suwannee River fulvic acid without using dual-spray approach. The major advantage of the calibrant proposed in this study is a lack of suppression of humic substances signals and maintenance of peak intensity distribution. The appropriate calibration resulted in an increased number of unambiguous identification in Suwannee River fulvic acid. Thanks to the higher mass accuracy, it was also possible to refine attribution of the CHOS species to hydrolysable tannins as opposed to the erroneous previous assignment to the condensed tannins.

How representative are dissolved organic matter (DOM) extracts? A comprehensive study of sorbent selectivity for DOM isolation

Solid phase extraction (SPE) has become a widespread method for isolating dissolved organic matter (DOM) of diverse origin such as fresh and marine waters. This study investigated the DOM extraction selectivity of 24 commercially available SPE sorbents under identical conditions (pH = 2, methanol elution) on the example of Suwannee River (SR) water and North Sea (NS) water by using DOC analysis and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Proton nuclear magnetic resonance (¹H NMR) spectroscopy was employed to assess leaching behavior, and HLB sorbent was found to leach substantially, among others. Variable DOC recoveries observed for SR DOM and NS DOM were primarily caused by the respective molecular composition, with subordinated and heterogeneous contributions of relative salinity. Scatter of average H/C and O/C elemental ratios and gross alignment in mass-edited H/C ratios according to five established coarse SPE characteristics was near identical for SR DOM and NS DOM. FTMS-based principal component analysis (PCA) provided essentially analogous alignment of SR DOM and NS DOM molecular compositions according to the five established groups of SPE classification, and corroborated the sorption-mechanism-based selectivity of DOM extraction in both cases. Evaluation of structural blanks and leaching of SPE cartridges requires NMR spectroscopy because FT-ICR mass spectrometry alone will not reveal inconspicuous displacements of continual bulk signatures caused by leaching of SPE resin constituents.

Enumeration of carboxyl groups carried on individual components of humic systems using deuteromethylation and Fourier transform mass spectrometry

Here, we report a novel approach to enumeration of carboxylic groups carried by individual molecules of humic substances using selective chemical modification and isotopic labeling (deuteromethylation) and high-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS). Esterification was conducted with a use of thionyl chloride-deuteromethanol reagent under mild conditions to avoid transesterification. The deuteromethylated products were subjected to solid phase extraction using PPL Bond Elute cartridges prior to FTICR MS analysis. An amount of carboxyl groups in the individual molecular component was estimated from the length of identified deuteromethylation series. The method allowed for discerning between compounds with close elemental compositions possessing different protolytic properties. We found that different carboxylic moieties occupy distinct regions in molecular space of humic substances (HS) projected onto Van Krevelen diagram. These locations do not depend on the source of the humic material and can be assigned to carboxyl-rich alicyclic molecules (5 to 6 COOH), hydrolyzable tannins (3-4 COOH), lignins (1 to 2 COOH), condensed tannins and lignans (0 to 1 COOH), and carbohydrates (0 COOH). At the same time, the alignment pattern of these carboxylated species along the structural evolution lines in Van Krevelen diagrams was characteristic to the specific transformation processes undergone by the humic materials in the different environments. The obtained data enable mapping of molecular ensemble of HS with regards to their specific acidic compartments and might be used for directed fractionation of HS. Graphical abstract Selective isotopic labeling followed by FTICR MS enables discerning between humic molecules with close elemental compositions carrying different numbers of carboxylic groups.

Supramolecular combinations of humic polyanions as potent microbicides with polymodal anti-HIV-activities

Anti-HIV potency of humic PAs is governed by scaffolds diversity.

Comprehensive structure-selective characterization of dissolved organic matter by reducing molecular complexity and increasing analytical dimensions

Deciphering the molecular codes of dissolved organic matter (DOM) improves our understanding of its role in the global element cycles and its active involvement in ecosystem services. This study demonstrates comprehensive characterization of DOM by an initial polarity-based stepwise solid phase extraction (SPE) with single methanol elution of the cartridges, but separate collection of equal aliquots of eluate. The reduction of molecular complexity in the individual DOM fractions attenuates intermolecular interactions and substantially increases the disposable resolution of any structure selective characterization. Suwannee River DOM (SR DOM) was used to collect five distinct SPE fractions with overall 91% DOC recovery. Optical spectroscopy (UV and fluorescence spectroscopy), high-field Fourier transform ion cyclotron mass spectrometry (FTICR MS) and nuclear magnetic resonance (NMR) spectroscopy showed analogous hierarchical clustering among the five eluates corroborating the robustness of this approach. Two abundant moderately hydrophobic fractions contained most of the SR DOM compounds, with substantial proportions of aliphatics, carboxylic-rich alicyclic molecules, carbohydrates and aromatics. A minor early eluting hydrophilic fraction was highly aliphatic and presented a large diversity of alicyclic carboxylic acids, whereas the two late eluting, minor hydrophobic fractions appeared as a largely defunctionalized mixture of aliphatic molecules. Comparative mass analysis showed that fractionation of SR DOM was governed by multiple molecular interactions depending on O/C ratio, molecular weight and aromaticity. The traditional optical indices SUVA₂₅₄ and fluorescence index (FI) indicated the relative aromaticity in agreement with FTICR mass and NMR spectra; the classical fluorescent peaks A and C were observed in all four latter eluates. This versatile approach can be easily expanded to preparative scale under field conditions, and transferred to different DOM sources and SPE conditions.

High field FT-ICR mass spectrometry for molecular characterization of snow board from Moscow regions

High field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry analysis of eight snow samples from Moscow city allowed us to identify more than 2000 various elemental compositions corresponding to regional air pollutants. The hierarchical cluster analysis (HCA) of the data showed good concordance of three main groups of samples with the main wind directions. The North-West group (A1) is represented by several homologous CHOS series of aliphatic organic aerosols. They may form as a result of enhanced photochemical reactions including oxidation of hydrocarbons with sulfonations due to higher amount of SO2 emissions in the atmosphere in this region. Group A2, corresponding to the South-East part of Moscow, contains large amount of oxidized hydrocarbons of different sources that may form during oxidation in atmosphere. These hydrocarbons appear correlated to emissions from traffic, neighboring oil refinery, and power plants. Another family of compounds specific for this region involves CHNO substances formed during oxidation processes including NOx and NO3 radical since emissions of NOx are higher in this part of the city. Group A3 is rich in CHO type of compounds with high H/C and low O/C ratios, which is characteristic of oxidized hydrocarbon-like organic aerosol. CHNO types of compounds in A3 group are probably nitro derivatives of condensed hydrocarbons such as PAH. This non-targeted profiling revealed site specific distribution of pollutants and gives a chance to develop new strategies in air quality control and further studies of Moscow environment.

Isotope-filtered nD NMR spectroscopy of complex mixtures to unravel the molecular structures of phenolic compounds in tagged soil organic matter

Unravelling structures of molecules contained in complex, chromatographically inseparable mixtures is a challenging task. Due to the number of overlapping resonances in NMR spectra of these mixtures, unambiguous chemical shift correlations attributable to individual molecules cannot be achieved and thus their structure determination is elusive by this technique. Placing a tag carrying an NMR active nucleus onto a subset of molecules enables (i) to eliminate signals from the non-tagged molecules, and (ii) to obtain a set of correlated chemical shifts and coupling constants belonging to a single molecular type. This approach provides an opportunity for structure determination without the need for compound separation. Focusing on the most abundant functional groups of natural organic matter molecules, the carboxyl and hydroxyl groups were converted into esters and ethers, respectively by introducing (13)CH3O groups. A set of (13)C-filtered nD NMR experiments was designed yielding structures/structural motives of tagged molecules. The relative sensitivity of these experiments was compared and a step-by-step guide how to use these experiments to analyse the structures of methylated phenolics is provided. The methods are illustrated using an operational fraction of soil organic matter, fulvic acid isolated from a Scottish peat bog. Analysis of 33 structures identified in this sample revealed a correlation between the position of the methoxy cross-peaks in the (1)H, (13)C HSQC spectra and the compound type. This information enables profiling of phenolic compounds in natural organic matter without the need to acquire a full set of experiments described here or access to high field cryoprobe NMR spectrometers.

Development of an in Situ NMR Photoreactor To Study Environmental Photochemistry

Photochemistry is a key environmental process directly linked to the fate, source, and toxicity of pollutants in the environment. This study explores two approaches for integrating light sources with nuclear magnetic resonance (NMR) spectroscopy: sample irradiation using a "sunlight simulator" outside the magnet versus direct irradiation of the sample inside the magnet. To assess their applicability, the in situ NMR photoreactors were applied to a series of environmental systems: an atmospheric pollutant (p-nitrophenol), crude oil extracts, and groundwater. The study successfully illustrates that environmentally relevant aqueous photochemical processes can be monitored in situ and in real time using NMR spectroscopy. A range of intermediates and degradation products were identified and matched to the literature. Preliminary measurements of half-lives were also obtained from kinetic curves. The sunlight simulator was shown to be the most suitable model to explore environmental photolytic processes in situ. Other light sources with more intense UV output hold potential for evaluating UV as a remediation alternative in areas such as wastewater treatment plants or oil spills. Finally, the ability to analyze the photolytic fate of trace chemicals at natural abundance in groundwater, using a cryogenic probe, demonstrates the viability of NMR spectroscopy as a powerful and complementary technique for environmental applications in general.

Geochemistry of Dissolved Organic Matter in a Spatially Highly Resolved Groundwater Petroleum Hydrocarbon Plume Cross-Section

At numerous groundwater sites worldwide, natural dissolved organic matter (DOM) is quantitatively complemented with petroleum hydrocarbons. To date, research has been focused almost exclusively on the contaminants, but detailed insights of the interaction of contaminant biodegradation, dominant redox processes, and interactions with natural DOM are missing. This study linked on-site high resolution spatial sampling of groundwater with high resolution molecular characterization of DOM and its relation to groundwater geochemistry across a petroleum hydrocarbon plume cross-section. Electrospray- and atmospheric pressure photoionization (ESI, APPI) ultrahigh resolution mass spectrometry (FT-ICR-MS) revealed a strong interaction between DOM and reactive sulfur species linked to microbial sulfate reduction, i.e., the key redox process involved in contaminant biodegradation. Excitation emission matrix (EEM) fluorescence spectroscopy in combination with Parallel Factor Analysis (PARAFAC) modeling attributed DOM samples to specific contamination traits. Nuclear magnetic resonance (NMR) spectroscopy evaluated the aromatic compounds and their degradation products in samples influenced by the petroleum contamination and its biodegradation. Our orthogonal high resolution analytical approach enabled a comprehensive molecular level understanding of the DOM with respect to in situ petroleum hydrocarbon biodegradation and microbial sulfate reduction. The role of natural DOM as potential cosubstrate and detoxification reactant may improve future bioremediation strategies.