1
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Mitschke N, Vemulapalli SPB, Dittmar T. Dissolved Organic Matter Contains Ketones Across a Wide Range of Molecular Formulas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:15587-15597. [PMID: 39163040 PMCID: PMC11375772 DOI: 10.1021/acs.est.4c02593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The carbonyl functionality of natural organic matter (NOM) is poorly constrained. Here, we treated Suwannee River NOM (SRNOM) with ammonium acetate and sodium cyanoborohydride to convert ketone-containing compounds by reductive amination to their corresponding primary amines. The total dissolved nitrogen content increased by up to 275% after amination. Up to 30% of the molecular formulas of SRNOM contained isomers with ketone functionalities as detected by ultrahigh-resolution mass spectrometry. Most of these isomers contained one or two keto groups. At least 3.5% of the oxygen in SRNOM was bound in ketone moieties. The conversion of reacted compounds increased linearly with O/H values of molecular formulas and was predictable from the elemental composition. The mean conversion rate of reacted compounds nearly followed a log-normal distribution. This distribution and the predictability of the proportion of ketone-containing isomers solely based on the molecular formula indicated a stochastic distribution of ketones across SRNOM compounds. We obtained isotopically labeled amines by using 15N-labeled ammonium acetate, facilitating the identification of reaction products and enabling NMR spectroscopic analysis. 1H,15N HSQC NMR experiments of derivatized samples containing less than 20 μg of nitrogen confirmed the predominant formation of primary amines, as expected from the reaction pathway.
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Affiliation(s)
- Nico Mitschke
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
| | - Sahithya Phani Babu Vemulapalli
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB) at the Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstraße 231, Oldenburg 26129, Germany
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2
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Wootton CA, Maillard J, Theisen A, Brabeck GF, Schat CL, Rüger CP, Afonso C, Giusti P. A Gated TIMS FTICR MS Instrument to Decipher Isomeric Content of Complex Organic Mixtures. Anal Chem 2024; 96:11343-11352. [PMID: 38973712 DOI: 10.1021/acs.analchem.4c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Modern research faces increasingly complex materials with a constant need for new analytical strategies that can provide deeper levels of chemical insight. Ultrahigh resolution mass spectrometry (MS), particularly Fourier transform ion cyclotron resonance (FTICR) MS, has provided a robust analytical foundation. However, MS alone offers limited structural information. Here, we present the first implementation and results from an FTICR MS with fully integrated dual accumulation analysis with gated trapped ion mobility spectrometry (gTIMS) capability. The drastically extended charge capacity and parallel accumulation facilitate the analysis of complex mixtures. We achieved a high dynamic range of 4 orders of magnitude within a single FTICR acquisition event. Simultaneously, the valuable linear relationship between the TIMS elution voltage and reduced mobility was retained over a wide mobility range. Benchmarking the instrument performance with Suwannee River fulvic acid (SRFA) by variable ramp gTIMS analysis allowed separation and unambiguous assignment of different charge state distributions. Application to bio-oils has proven the capability to distinguish the isomeric diversity in these ultracomplex samples, while maintaining the expected FTICR MS resolving power and mass accuracy. Valuable information about the molecular distribution, isomeric diversity, and main molecular differences could directly be extracted within the analysis time of a classical "dilute and shoot" direct infusion experiment. The development of this fully integrated and flexible gTIMS with FTICR MS analysis possesses the potential to significantly change the current landscape of high-resolution mass spectrometric analysis of complex mixtures through the added insight of isomeric complexity afforded by TIMS. The exploration of the added IMS dimension promises transformative effects across diverse fields including energy transition, environmental studies, and biological research.
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Affiliation(s)
| | - Julien Maillard
- TotalEnergies One Tech, R&D, Downstream Processes & Polymers, TotalEnergies Research & Technology Gonfreville, BP 27, 76700 Harfleur, France
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Alina Theisen
- Bruker Daltonics GmbH & Co. Kg, 28359 Bremen, Germany
| | | | | | - Christopher P Rüger
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Carlos Afonso
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, 76000 Rouen, France
| | - Pierre Giusti
- TotalEnergies One Tech, R&D, Downstream Processes & Polymers, TotalEnergies Research & Technology Gonfreville, BP 27, 76700 Harfleur, France
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, 76000 Rouen, France
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3
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Plamper P, Lechtenfeld OJ, Herzsprung P, Groß A. A Temporal Graph Model to Predict Chemical Transformations in Complex Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18116-18126. [PMID: 37159837 PMCID: PMC10666529 DOI: 10.1021/acs.est.3c00351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/11/2023]
Abstract
Dissolved organic matter (DOM) is a complex mixture of thousands of natural molecules that undergo constant transformation in the environment, such as sunlight induced photochemical reactions. Despite molecular level resolution from ultrahigh resolution mass spectrometry (UHRMS), trends of mass peak intensities are currently the only way to follow photochemically induced molecular changes in DOM. Many real-world relationships and temporal processes can be intuitively modeled using graph data structures (networks). Graphs enhance the potential and value of AI applications by adding context and interconnections allowing the uncovering of hidden or unknown relationships in data sets. We use a temporal graph model and link prediction to identify transformations of DOM molecules in a photo-oxidation experiment. Our link prediction algorithm simultaneously considers educt removal and product formation for molecules linked by predefined transformation units (oxidation, decarboxylation, etc.). The transformations are further weighted by the extent of intensity change and clustered on the graph structure to identify groups of similar reactivity. The temporal graph is capable of identifying relevant molecules subject to similar reactions and enabling to study their time course. Our approach overcomes previous data evaluation limitations for mechanistic studies of DOM and leverages the potential of temporal graphs to study DOM reactivity by UHRMS.
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Affiliation(s)
- Philipp Plamper
- Anhalt
University of Applied Sciences, Department Computer Science and Languages, Lohmannstraße 23, Köthen 06366, Germany
| | - Oliver J. Lechtenfeld
- Helmholtz
Centre for Environmental Research − UFZ, Department of Analytical Chemistry, Research Group
BioGeoOmics, Permoserstraße
15, Leipzig 04318, Germany
- ProVIS
- Centre for Chemical Microscopy, Helmholtz Centre for Environmental
Research - UFZ, Permoserstraße
15, Leipzig 04318, Germany
| | - Peter Herzsprung
- Helmholtz
Centre for Environmental Research − UFZ, Department of Lake Research, Brückstraße 3a, Magdeburg 39114, Germany
| | - Anika Groß
- Anhalt
University of Applied Sciences, Department Computer Science and Languages, Lohmannstraße 23, Köthen 06366, Germany
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4
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Glöckler D, Harir M, Schmitt-Kopplin P, Elsner M, Bakkour R. Selectivity of β-Cyclodextrin Polymer toward Aquatic Contaminants: Insights from Ultrahigh-Resolution Mass Spectrometry of Dissolved Organic Matter. Anal Chem 2023; 95:15505-15513. [PMID: 37831967 DOI: 10.1021/acs.analchem.3c01394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Selectivity in solid-phase extraction (SPE) materials has become increasingly important for analyte enrichment in sensitive analytical workflows to alleviate detrimental matrix effects. Molecular-level investigation of matrix constituents, which are preferentially extracted or excluded, can provide the analytical chemist with valuable information to learn about their control on sorbent selectivity. In this work, we employ nontargeted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to elucidate the molecular chemodiversity of freshwater-derived dissolved organic matter (DOM) extracted by the selective model sorbent β-cyclodextrin polymer (β-CDP) in comparison to conventional, universal SPE sorbents (i.e., Oasis HLB, Supel-Select HLB, and LiChrolut EN). Statistical analysis of MS data corroborated the highly selective nature of β-CDP by revealing the extracted DOM spectra that are most dissimilar to original compositions. We found that its selectivity was characterized by pronounced discrimination against highly oxygenated and unsaturated DOM compounds, which were associated with the classes of lignin-like, tannin-like, and carboxylic-rich alicyclic molecules. In contrast, conventional sorbents excluded less highly oxygenated compounds and showed a more universal extraction behavior for a wide range of DOM compositional space. We lay these findings in a larger context that aids the analyst in obtaining an a priori estimate of sorbent selectivity toward any target analyte of interest serving thereby an optimization of sample preparation. This study highlights the great value of nontargeted ultrahigh-resolution MS for better understanding of targeted analytics and provides new insights into the selective sorption behavior of novel sorbents.
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Affiliation(s)
- David Glöckler
- TUM School of Natural Sciences, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Garching 85748 , Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Neuherberg 85764, Germany
- TUM School of Life Sciences, Chair of Analytical Food Chemistry, Technical University of Munich, Freising 85354, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Neuherberg 85764, Germany
- TUM School of Life Sciences, Chair of Analytical Food Chemistry, Technical University of Munich, Freising 85354, Germany
| | - Martin Elsner
- TUM School of Natural Sciences, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Garching 85748 , Germany
| | - Rani Bakkour
- TUM School of Natural Sciences, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Garching 85748 , Germany
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5
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Lv J, Huang Z, Luo L, Zhang S, Wang Y. Advances in Molecular and Microscale Characterization of Soil Organic Matter: Current Limitations and Future Prospects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12793-12810. [PMID: 36037253 DOI: 10.1021/acs.est.2c00421] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soil organic matter (SOM) comprises a continuum of organic materials from granular organic debris to small organic molecules and contains more organic carbon than global vegetation and the atmosphere combined. It has remarkable effects on soil ecological functions and the global carbon cycle as well as the fate of pollutants in the terrestrial ecosystem. Therefore, characterization of SOM is an important topic in soil science, ecology, and environmental science. Chemical complexity and spatial heterogeneity are by far the two biggest challenges to our understanding of SOM. Recent developments in analytical techniques and methods provide the opportunity to reveal SOM composition at the molecular level and to observe its distribution in soils at micro- and nanoscales, which have greatly improved our understanding of SOM. This paper reviews the outstanding advances in SOM characterization regarding these two issues from target and nontarget analyses comprising molecular marker analysis, ultrahigh-resolution mass spectrometry analysis, and in situ microscopic imaging techniques such as synchrotron-based spectromicroscopy, nanoscale secondary ion mass spectrometry, and emerging electron and optical microscopic imaging techniques. However, current techniques and methods remain far from unlocking the unknown properties of SOM. We systematically point out the limitations of the current technologies and outline the future prospects for comprehensive characterization of SOM at the molecular level and micro- and nanoscales, paying particular attention to issues of environmental concern.
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Affiliation(s)
- Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoquan Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Guangdong Key Laboratory of Contaminated Site Environmental Management and Remediation, Guangdong Provincial Academy of Environmental Science, Guangzhou, Guangdong 510045, China
| | - Lei Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Berggren M, Guillemette F, Bieroza M, Buffam I, Deininger A, Hawkes JA, Kothawala DN, LaBrie R, Lapierre J, Murphy KR, Al‐Kharusi ES, Rulli MPD, Hensgens G, Younes H, Wünsch UJ. Unified understanding of intrinsic and extrinsic controls of dissolved organic carbon reactivity in aquatic ecosystems. Ecology 2022; 103:e3763. [PMID: 35612376 PMCID: PMC9540823 DOI: 10.1002/ecy.3763] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/18/2022] [Indexed: 11/15/2022]
Abstract
Despite our growing understanding of the global carbon cycle, scientific consensus on the drivers and mechanisms that control dissolved organic carbon (DOC) turnover in aquatic systems is lacking, hampered by the mismatch between research that approaches DOC reactivity from either intrinsic (inherent chemical properties) or extrinsic (environmental context) perspectives. Here we propose a conceptual view of DOC reactivity in which the combination of intrinsic and extrinsic factors controls turnover rates and determines which reactions will occur. We review three major types of reactions (biological, photochemical, and flocculation) from an intrinsic chemical perspective and further define the environmental features that modulate the expression of chemically inherent reactivity potential. Finally, we propose hypotheses of how extrinsic and intrinsic factors together shape patterns in DOC turnover across the land-to-ocean continuum, underscoring that there is no intrinsic DOC reactivity without environmental context. By acknowledging the intrinsic-extrinsic control duality, our framework intends to foster improved modeling of DOC reactivity and its impact on ecosystem services.
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Affiliation(s)
- Martin Berggren
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | - François Guillemette
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois‐RivièresQuébecCanada
- Groupe de recherche interuniversitaire en limnologie (GRIL)MontréalQuébecCanada
| | - Magdalena Bieroza
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Ishi Buffam
- Department of Landscape Architecture, Planning and ManagementSwedish University of Agricultural SciencesAlnarpSweden
| | - Anne Deininger
- Norwegian Institute for Water Research (NIVA)OsloNorway
- Centre for Coastal Research (CCR), University of AgderKristiansandNorway
| | | | | | - Richard LaBrie
- Groupe de recherche interuniversitaire en limnologie (GRIL)MontréalQuébecCanada
- Département des Sciences biologiquesUniversité de MontréalMontréalQuebecCanada
- Interdisciplinary Environmental Research CentreFreibergGermany
| | - Jean‐François Lapierre
- Groupe de recherche interuniversitaire en limnologie (GRIL)MontréalQuébecCanada
- Département des Sciences biologiquesUniversité de MontréalMontréalQuebecCanada
| | - Kathleen R. Murphy
- Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
| | - Enass S. Al‐Kharusi
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | - Mayra P. D. Rulli
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | - Geert Hensgens
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | - Hani Younes
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | - Urban J. Wünsch
- Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
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7
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Simon C, Dührkop K, Petras D, Roth VN, Böcker S, Dorrestein PC, Gleixner G. Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11027-11040. [PMID: 35834352 PMCID: PMC9352317 DOI: 10.1021/acs.est.2c01332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 05/30/2023]
Abstract
Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS2 experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11 477 Δm features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δm matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.
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Affiliation(s)
- Carsten Simon
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Kai Dührkop
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Daniel Petras
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
- CMFI
Cluster of Excellence, Interfaculty Institute of Microbiology and
Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Vanessa-Nina Roth
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Sebastian Böcker
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
| | - Gerd Gleixner
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
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8
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Zherebker A, Rukhovich GD, Sarycheva A, Lechtenfeld OJ, Nikolaev EN. Aromaticity Index with Improved Estimation of Carboxyl Group Contribution for Biogeochemical Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2729-2737. [PMID: 35084826 DOI: 10.1021/acs.est.1c04575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Natural organic matter (NOM) components measured with ultrahigh-resolution mass spectrometry (UHRMS) are often assessed by molecular formula-based indices, particularly related to their aromaticity, which are further used as proxies to explain biogeochemical reactivity. An aromaticity index (AI) is calculated mostly with respect to carboxylic groups abundant in NOM. Here, we propose a new constrained AIcon based on the measured distribution of carboxylic groups among individual NOM components obtained by deuteromethylation and UHRMS. Applied to samples from diverse sources (coal, marine, peat, permafrost, blackwater river, and soil), the method revealed that the most probable number of carboxylic groups was two, which enabled to set a reference point n = 2 for carboxyl-accounted AIcon calculation. The examination of the proposed AIcon showed the smallest deviation to the experimentally determined index for all NOM samples under study as well as for individual natural compounds obtained from the Coconut database. In particular, AIcon performed better than AImod for all compound classes in which aromatic moieties are expected: aromatics, condensed aromatics, and unsaturated compounds. Therefore, AIcon referenced with two carboxyl groups is preferred over conventional AI and AImod for biogeochemical studies where the aromaticity of compounds is important to understand the transformations and fate of NOM compounds.
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Affiliation(s)
| | - Gleb D Rukhovich
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research─UFZ, Leipzig DE-04318, Germany
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9
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Ma G, Xu H, Yang X, An G, Yang Q, Wang X, Wang D. Molecular investigation on changing behaviors of natural organic matter by coagulation with non-targeting screen using high-resolution mass spectrometry. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127408. [PMID: 34653857 DOI: 10.1016/j.jhazmat.2021.127408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Natural organic matter (NOM) can tremendously influence the purification efficiency of the drinking water treatment process. Coagulation was the first and primary process of NOM removal in the drinking water treatment process. The interaction between coagulants and NOM molecules remains unclear. Three typical coagulants (Al13, FeCl3, and AlCl3) were used to investigate the effects on NOM removal. The measurement of NOM was conducted using 15 T Electrospray Ionization coupled Fourier-Transform-Ion Cyclotron Resonance Mass Spectrometry (ESI-FT-ICR MS). The coagulation process altered the mass peak numbers as well as relative intensity of the peaks which were positively correlated with TOC value. The lignin-like compound was the most abundant moiety in raw water. Al-based coagulants remove more unsaturated larger compounds (lower KMD and higher carbon number). Al13 remove the unsaturated hydrocarbons preferably. FeCl3 is more reactive with NOM molecules and removes more fully saturated compounds. These findings revealed the coagulation removal mechanism of NOM with different structural characteristics and advise the practical use of coagulants for various raw water with different NOM characteristics.
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Affiliation(s)
- Gefei Ma
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaofang Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyu An
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qinxue Yang
- Faculty Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xi Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dongsheng Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18, Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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10
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Fu QL, Fujii M, Watanabe A, Kwon E. Formula Assignment Algorithm for Deuterium-Labeled Ultrahigh-Resolution Mass Spectrometry: Implications of the Formation Mechanism of Halogenated Disinfection Byproducts. Anal Chem 2022; 94:1717-1725. [PMID: 35019276 DOI: 10.1021/acs.analchem.1c04298] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ultrahigh-resolution mass spectrometry (UHR-MS) coupled with isotope labeling has attracted significant attention in elucidating the mechanisms of the transformation of dissolved organic matter (DOM). Herein, we developed a novel formula assignment algorithm based on deuterium (D)-labeled UHR-MS, namely, FTMSDeu, for the first time. This algorithm was employed to determine the precursor molecules of halogenated disinfection byproducts (Xn-DBPs) and to evaluate the relative contribution of electrophilic addition and substitution reactions in Xn-DBP formation according to the H/D exchange of DOM molecules. Further, tandem mass spectrometry with homologous-based network analysis was used to validate the formula assignment accuracy of FTMSDeu in the identification of iodinated disinfection byproducts. Electrophilic substitution accounted for 82-98, 71-89, and 43-45% of the formation for Cl-, Br-, and I-containing Xn-DBPs, respectively, indicating the dominant role of the electrophilic substitution in chlorinated disinfection byproducts with low Br and I concentrations. The absence of putative precursors in some Xn-DBPs also suggests that Xn-DBP formation includes secondary reactions (e.g., oxidation and hydrolysis) in addition to the electrophilic addition and/or substitution of halogens. These findings highlight the significance of isotopically labeled UHR-MS techniques in revealing the transformation of DOM in natural and engineered systems.
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Affiliation(s)
- Qing-Long Fu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.,Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan 430074, China
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan
| | - Akari Watanabe
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-Ku, Sendai 980-8578, Japan
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11
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Mikhnevich T, Vyatkina (Turkova) AV, Grigorenko VG, Rubtsova MY, Rukhovich GD, Letarova MA, Kravtsova DS, Vladimirov SA, Orlov AA, Nikolaev EN, Zherebker A, Perminova IV. Inhibition of Class A β-Lactamase (TEM-1) by Narrow Fractions of Humic Substances. ACS OMEGA 2021; 6:23873-23883. [PMID: 34568667 PMCID: PMC8459357 DOI: 10.1021/acsomega.1c02841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance is a global threat. The use of biologically active natural products alone or in combination with the clinically proven antimicrobial agents might be a useful strategy to fight the resistance. The scientific hypotheses of this study were twofold: (1) the natural humic substances rich in dicarboxyl, phenolic, heteroaryl, and other fragments might possess inhibitory activity against β-lactamases, and (2) this inhibitory activity might be linked to the molecular composition of the humic ensemble. To test these hypotheses, we used humic substances (HS) from different sources (coal, peat, and soil) and of different fractional compositions (humic acids, hymatomelanic acids, and narrow fractions from solid-phase extraction) for inhibiting serine β-lactamase TEM-1. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) was used to characterize the molecular composition of all humic materials used in this study. The kinetic assay with chromogenic substrate CENTA was used for assessment of inhibitory activity. The inhibition data have shown that among all humic materials tested, a distinct activity was observed within apolar fractions of hymatomelanic acid isolated from lignite. The decrease in the hydrolysis rate in the presence of most active fractions was 42% (with sulbactam-87%). Of particular importance is that these very fractions caused a synergistic effect (2-fold) for the combinations with sulbactam. Linking the observed inhibition effects to molecular composition revealed the preferential contribution of low-oxidized aromatic and acyclic components such as flavonoid-, lignin, and terpenoid-like molecules. The binding of single low-molecular-weight components to the cryptic allosteric site along with supramolecular interactions of humic aggregates with the protein surface could be considered as a major contributor to the observed inhibition. We believe that fine fractionation of hydrophobic humic materials along with molecular modeling studies on the interaction between humic molecules and β-lactamases might contribute to the development of novel β-lactamase inhibitors of humic nature.
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Affiliation(s)
- Tatyana
A. Mikhnevich
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | | | - Vitaly G. Grigorenko
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | - Maya Yu. Rubtsova
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | - Gleb D. Rukhovich
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | - Maria A. Letarova
- Vinogradsky
Institute of Microbiology, RC Biotechnology of RAS, Prospekt 60-Letiya Oktyabrya, 7,
bldg 2, Moscow 117312, Russia
| | - Darya S. Kravtsova
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | - Sergey A. Vladimirov
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
| | - Alexey A. Orlov
- Skolkovo
Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Evgeny N. Nikolaev
- Skolkovo
Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Alexander Zherebker
- Skolkovo
Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Irina V. Perminova
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie gory 1, bld. 3, Moscow 119991, Russia
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12
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Formation of Humic-Like Substances during the Technological Process of Lignohumate® Synthesis as a Function of Time. SEPARATIONS 2021. [DOI: 10.3390/separations8070096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The composition, structure, and biological activity of humic-like substances (HLS) synthesized in the process of lignosulfonate conversion for the production of the humic product Lignohumate® (LH) were examined. It is shown that during the hydrolytic-oxidative process, the transformation of raw material and accumulation of HLS occur. Data on the chemical (elemental content, functional groups, FTIR) and spectral (absorbance and fluorescence) parameters and biological activity (in phytotest) combined with PCA show that the LH samples can be divided into three groups, depending on the duration of synthesis: initial raw material (0-time sample); “young” HLS (15–30 min), and “mature” HLS in 45–120 min of treatment. During the first 30 min, reactions similar to the ones that occur during lignin humification in nature take place: depolymerization, oxidative carboxylation, and further polycondensation with the formation and accumulation of HLS. After 45–60 min, the share of HLS reaches a maximum, and its composition stabilizes. Biological activity reaches a maximum after 45–60 min of treatment, and at that stage, the further synthesis process can be stopped. Further processing (up to 2 h and more) does not provide any added value to the humic product.
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13
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Zherebker A, Kostyukevich Y, Volkov DS, Chumakov RG, Friederici L, Rüger CP, Kononikhin A, Kharybin O, Korochantsev A, Zimmermann R, Perminova IV, Nikolaev E. Speciation of organosulfur compounds in carbonaceous chondrites. Sci Rep 2021; 11:7410. [PMID: 33795703 PMCID: PMC8016918 DOI: 10.1038/s41598-021-86576-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
Despite broad application of different analytical techniques for studies on organic matter of chondrite meteorites, information about composition and structure of individual compounds is still very limited due to extreme molecular diversity of extraterrestrial organic matter. Here we present the first application of isotopic exchange assisted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis of alkali extractable fraction of insoluble organic matter (IOM) of the Murchison and Allende meteorites. This allowed us to determine the individual S-containing ions with different types of sulfur atoms in IOM. Thiols, thiophenes, sulfoxides, sulfonyls and sulfonates were identified in both samples but with different proportions, which contribution corroborated with the hydrothermal and thermal history of the meteorites. The results were supported by XPS and thermogravimetric analysis coupled to FTICR MS. The latter was applied for the first time for analysis of chondritic IOM. To emphasize the peculiar extraterrestrial origin of IOM we have compared it with coal kerogen, which is characterized by the comparable complexity of molecular composition but its aromatic nature and low oxygen content can be ascribed almost exclusively to degradation of biomacromolecules.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Dmitry S Volkov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Lukas Friederici
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany
| | - Alexey Kononikhin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025.,V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Alexander Korochantsev
- Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Kosygina 19, Moscow, Russia, 119334
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany.,Joint Mass Spectrometry Centre of Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025.
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14
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Zherebker AY, Rukhovich GD, Kharybin ON, Fedoros EI, Perminova IV, Nikolaev EN. Fourier transform ion cyclotron resonance mass spectrometry for the analysis of molecular composition and batch-to-batch consistency of plant-derived polyphenolic ligands developed for biomedical application. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8850. [PMID: 32492216 DOI: 10.1002/rcm.8850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
UNLABELLED Complex plant-derived polyphenols are promising for biomedical application. Their high complexity prevents the use of conventional pharmacopoeia techniques to perform quality control. The goal of this study was to apply ultra-high-resolution mass spectrometry to evaluate the batch-to-batch consistency of the molecular composition of a polyphenolic ligand using appropriate statistical metrics. METHODS Polyphenols were obtained by hydrolyzed-lignin oxidation. Manufacturing was performed under a range of reaction conditions: heating cycles, oxygen flows, purification. Direct-injection Fourier transform ion cyclotron resonance mass spectrometry (DI FTICR-MS) was applied to analyze reaction products. For pairwise comparison Jaccard and Tanimoto similarities calculations were proposed. In addition, principal component analysis (PCA) was applied for sample grouping based on the molecular class contributions. RESULTS FTICR-MS analysis revealed moderate Jaccard similarity of products synthesized under the same conditions, which shared about 50% of the formulae calculated in each sample. The intensity-based Tanimoto index indicated high similarity of major components distribution of samples synthesized under standard conditions, while products obtained with variations in synthetic conditions were significantly different. PCA of molecular class contributions showed similar grouping with a high cumulative score. CONCLUSIONS FTICR-MS provides robust metrics for the examination of batch-to-batch consistency of synthetic polyphenol materials. This approach can be proposed for the analysis of reference samples and for development of complementary methods for quality control of medicinal agents based on various biologically active matrices.
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Affiliation(s)
- Alexander Ya Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Gleb D Rukhovich
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg N Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg, 197758, Russia
- Nobel LTD, Saint-Petersburg, 192012, Russia
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
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15
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Patriarca C, Balderrama A, Može M, Sjöberg PJR, Bergquist J, Tranvik LJ, Hawkes JA. Investigating the Ionization of Dissolved Organic Matter by Electrospray. Anal Chem 2020; 92:14210-14218. [PMID: 32940031 PMCID: PMC7584329 DOI: 10.1021/acs.analchem.0c03438] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Electrospray
ionization (ESI) operating in the negative mode coupled
to high-resolution mass spectrometry is the most popular technique
for the characterization of dissolved organic matter (DOM). The vast
molecular heterogeneity and the functional group diversity of this
complex mixture prevents the efficient ionization of the organic material
by a single ionization source, so the presence of uncharacterized
material is unavoidable. The extent of this poorly ionizable pool
of carbon is unknown, is presumably variable between samples, and
can only be assessed by the combination of analysis with a uniform
detection method. Charged aerosol detection (CAD), whose response
is proportional to the amount of nonvolatile material and is independent
from the physicochemical properties of the analytes, is a suitable
candidate. In this study, a fulvic acid mixture was fractionated and
analyzed by high-pressure liquid chromatography–mass spectrometry
in order to investigate the polarity and size distributions of highly
and poorly ionizable material in the sample. Additionally, DOM samples
of terrestrial and marine origins were analyzed to evaluate the variability
of these pools across the land–sea aquatic continuum. The relative
response factor values indicated that highly ionizable components
of aquatic DOM mixtures are more hydrophilic and have lower molecular
weight than poorly ionizable components. Additionally, a discrepancy
between the samples of terrestrial and marine origins was found, indicating
that marine samples are better represented by ESI than terrestrial
samples, which have an abundant portion of hydrophobic poorly ionizable
material.
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Affiliation(s)
- Claudia Patriarca
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden
| | - Andrea Balderrama
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden.,Limnology, Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
| | - Martina Može
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden
| | - Per J R Sjöberg
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden
| | - Lars J Tranvik
- Limnology, Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
| | - Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, 75237 Uppsala, Sweden
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16
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Zherebker A, Yakimov B, Rubekina A, Kharybin O, Fedoros EI, Perminova IV, Shirshin E, Nikolaev EN. Photoreactivity of humic-like polyphenol material under irradiation with different wavelengths explored by FTICR MS and deuteromethylation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:292-300. [PMID: 32264711 DOI: 10.1177/1469066720917067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The goal of this study was to establish reactivity of lignin-derived synthetic polyphenolic material under irradiation by ultraviolet (254 nm) and visible (460 and 525 nm) light in order to deeper examine relationships between the optical properties of this complex mixture and its individual constituents. In all photoirradiation experiments, blue shift of the fluorescence spectrum was observed. We aimed at understanding whether these changes could be explained on the basis of the chromophore interactions hypothesis, which implies destruction of electron-acceptor pairs via free radical transformations to be responsible for the alteration of optical properties. For this, changes in molecular composition were explored by Fourier transform ion cyclotron resonance mass spectrometry. Irradiation with UV resulted in a pronounced oxidation of polyphenols, which was manifested in the van Krevelen diagram by the formation of components with higher O/C ratio. At the same time, irradiation by visible light had led to the appearance of more condensed molecules depleted of oxygen. Consideration of changes in relative contribution of 500 most abundant components in polyphenol materials revealed higher transformation yields under UV light as compared to the visible light. Further studies using deuteromethylation followed by Fourier transform ion cyclotron resonance mass spectrometry enabled to enumerate the number of carboxylic groups in individual components of the parent polyphenol material. It was shown that at all wavelengths irradiation mainly impacted carboxylic-rich unsaturated and aromatic compounds, which can be considered as strong electron-acceptors. We suggest that their transformation is responsible for the blue shift of fluorescence spectrum, thus emphasizing the role of chromophore interaction mechanism of the optical properties formation.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Boris Yakimov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Rubekina
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg, Russia
- Nobel LTD, Saint-Petersburg, Russia
| | - I V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny Shirshin
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
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17
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Zherebker A, Lechtenfeld OJ, Sarycheva A, Kostyukevich Y, Kharybin O, Fedoros EI, Nikolaev EN. Refinement of Compound Aromaticity in Complex Organic Mixtures by Stable Isotope Label Assisted Ultrahigh-Resolution Mass Spectrometry. Anal Chem 2020; 92:9032-9038. [PMID: 32484343 DOI: 10.1021/acs.analchem.0c01208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a unique opportunity for molecular analysis of natural complex mixtures. In many geochemical and environmental studies structure-propertry relations are based solely on the elemental compositional information. Several calculated parameters were proposed to increase reliability of structural attribution, among which aromaticity indices (AI and AImod) are widely used. Herein, we applied a combination of selective labeling reactions in order to obtain direct structural information on the individual components of lignin-derived polyphenolic material. Carboxylic (COOH), carbonyl (C═O), and hydroxyl (OH) groups were enumerated by esterification, reducing, and acetylation reactions, respectively, followed by FTICR MS analyses. Obtained information was enabled to constrain aromaticity accounting for the carbon skeleton only. We found that actual aromaticity of components may be both higher or lower than approximated values depending on the abundance of COOH, C═O, and OH groups. The results are of importance for the geochemical community studying terrestrial NOM with structural gradients.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig DE-04318, Germany
| | - Anastasia Sarycheva
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia.,Nobel LTD, Saint-Petersburg 192012, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
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18
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Hawkes JA, Sjöberg PJR, Bergquist J, Tranvik LJ. Complexity of dissolved organic matter in the molecular size dimension: insights from coupled size exclusion chromatography electrospray ionisation mass spectrometry. Faraday Discuss 2020; 218:52-71. [PMID: 31120465 DOI: 10.1039/c8fd00222c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper investigates the relationship between apparent size distribution and molecular complexity of dissolved organic matter from the natural environment. We used a high pressure size exclusion chromatography (HPSEC) method coupled to UV-Vis diode array detection (UV-DAD) and electrospray ionisation mass spectrometry (ESI-MS) in order to compare the apparent size of natural organic matter, determined by HPSEC-UV and the molecular mass determined online by ESI-MS. We found that there was a clear discrepancy between the two methods, and found evidence for an important pool of organic matter that has a strong UV absorbance and no ESI-MS signal. Contrary to some previous research, we found no evidence that apparently high molecular weight organic matter is constituted by aggregates of low molecular weight (<1000 Da) material. Furthermore, our results suggest that the majority of apparent size variability within the ESI ionisable pool of organic matter is due to secondary interaction and exclusion effects on the HPSEC column, and not true differences in hydrodynamic size or intermolecular aggregation.
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Affiliation(s)
- J A Hawkes
- Analytical Chemistry, Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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19
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Zherebker A, Shirshin E, Rubekina A, Kharybin O, Kononikhin A, Kulikova NA, Zaitsev KV, Roznyatovsky VA, Grishin YK, Perminova IV, Nikolaev EN. 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. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2667-2677. [PMID: 32045519 DOI: 10.1021/acs.est.9b05298] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
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 pKa 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.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny Shirshin
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna Rubekina
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
| | - Alexey Kononikhin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
| | - Natalia A Kulikova
- Department of Soil Science, Lomonosov Moscow State University, Moscow, 119991, Russia
- Federal Research Center "Fundamentals of Biotechnology", Bakh Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Kirill V Zaitsev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Yuri K Grishin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
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20
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Orlov AA, Zherebker A, Eletskaya AA, Chernikov VS, Kozlovskaya LI, Zhernov YV, Kostyukevich Y, Palyulin VA, Nikolaev EN, Osolodkin DI, Perminova IV. Examination of molecular space and feasible structures of bioactive components of humic substances by FTICR MS data mining in ChEMBL database. Sci Rep 2019; 9:12066. [PMID: 31427609 PMCID: PMC6700089 DOI: 10.1038/s41598-019-48000-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 07/29/2019] [Indexed: 01/08/2023] Open
Abstract
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.
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Affiliation(s)
- Alexey A Orlov
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anastasia A Eletskaya
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Department of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Liubov I Kozlovskaya
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Yury V Zhernov
- State Research Center "Institute of Immunology" of the Federal Medical-Biological Agency of Russia, Moscow, 115478, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Dmitry I Osolodkin
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia.
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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21
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Kostyukevich Y, Kitova A, Zherebker A, Rukh S, Nikolaev E. Investigation of the archeological remains using ultrahigh resolution mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:391-396. [PMID: 30939934 DOI: 10.1177/1469066719840287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Investigation of the archeological material at the molecular level can reveal the composition of ancient paint, balsamic material, reveal cooking recipes, etc. High-resolution mass spectrometry is a powerful technique with underestimated potential for archeology. Here, we present the investigation of the 3000-year-old archeological remains, identified as parts of internal organs of an Egyptian mummy, using high-resolution Orbitrap mass spectrometry. We observed a diverse number of oxidized classes of compounds: O, O2, O3, O4, O5, N, NO, NO2, NO3, NO4, NO5, N2O, N2O2. Such chemical composition is unusual and we never observed it in our previous studies of petroleum, humic substances, products of wood pyrolysis or other natural complex mixtures. It is possible that such compounds are formed via biodegradation of lipids and other organic material used for funeral rites. We did not observe evidence of the presence of mineral bitumen, although there are many historical records of the use of mineral bitumen for mummification.
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Affiliation(s)
- Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Alexandra Kitova
- 3 Center for Egyptological Studies of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zherebker
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Shah Rukh
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
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22
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Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry. Anal Bioanal Chem 2019; 411:3331-3339. [DOI: 10.1007/s00216-019-01802-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/19/2019] [Accepted: 03/22/2019] [Indexed: 10/26/2022]
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23
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Zherebker A, Shirshin E, Kharybin O, Kostyukevich Y, Kononikhin A, Konstantinov AI, Volkov D, Roznyatovsky VA, Grishin YK, Perminova IV, Nikolaev E. 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. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12179-12187. [PMID: 30335379 DOI: 10.1021/acs.jafc.8b04079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
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.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
| | - Evgeny Shirshin
- Department of Physics , Lomonosov Moscow State University , Leninskie Gory 1/2 , 119991 Moscow , Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Orekhovich Institute of Biomedical Chemistry , Russian Academy of Sciences , Pogodinskaya Ulitsa 10 , 119121 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
| | - Andrey I Konstantinov
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Dmitry Volkov
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | | | - Yuri K Grishin
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Irina V Perminova
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Orekhovich Institute of Biomedical Chemistry , Russian Academy of Sciences , Pogodinskaya Ulitsa 10 , 119121 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
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24
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Kostyukevich Y, Acter T, Zherebker A, Ahmed A, Kim S, Nikolaev E. Hydrogen/deuterium exchange in mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:811-853. [PMID: 29603316 DOI: 10.1002/mas.21565] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 05/22/2023]
Abstract
The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | - Thamina Acter
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
- Green Nano Center, Kyungpook National University, Daegu, Republic of Korea
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
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25
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Hawkes JA, Radoman N, Bergquist J, Wallin MB, Tranvik LJ, Löfgren S. Regional diversity of complex dissolved organic matter across forested hemiboreal headwater streams. Sci Rep 2018; 8:16060. [PMID: 30375497 PMCID: PMC6207752 DOI: 10.1038/s41598-018-34272-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/03/2018] [Indexed: 11/30/2022] Open
Abstract
Dissolved organic matter (DOM) from soils enters the aquatic environment via headwater streams. Thereafter, it is gradually transformed, removed by sedimentation, and mineralised. Due to the proximity to the terrestrial source and short water residence time, the extent of transformation is minimal in headwaters. DOM has variable composition across inland waters, but the amount of variability in the terrestrial end member is unknown. This gap in knowledge is crucial considering the potential impact large variability would have on modelling DOM degradation. Here, we used a novel liquid chromatography –mass spectrometry method to characterise DOM in 74 randomly selected, forested headwater streams in an 87,000 km2 region of southeast Sweden. We found a large degree of sample similarity across this region, with Bray-Curtis dissimilarity values averaging 8.4 ± 3.0% (mean ± SD). The identified variability could be reduced to two principle coordinates, correlating to varying groundwater flow-paths and regional mean temperature. Our results indicate that despite reproducible effects of groundwater geochemistry and climate, the composition of DOM is remarkably similar across catchments already as it leaves the terrestrial environment, rather than becoming homogeneous as different headwaters and sub-catchments mix.
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Affiliation(s)
- Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
| | - Nikola Radoman
- Analytical Chemistry, Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.,Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Marcus B Wallin
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - Lars J Tranvik
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Stefan Löfgren
- Department of Aquatic Sciences and Assessment; Section for Geochemistry and Hydrology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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26
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Fedoros EI, Orlov AA, Zherebker A, Gubareva EA, Maydin MA, Konstantinov AI, Krasnov KA, Karapetian RN, Izotova EI, Pigarev SE, Panchenko AV, Tyndyk ML, Osolodkin DI, Nikolaev EN, Perminova IV, Anisimov VN. Novel water-soluble lignin derivative BP-Cx-1: identification of components and screening of potential targets in silico and in vitro. Oncotarget 2018; 9:18578-18593. [PMID: 29719628 PMCID: PMC5915095 DOI: 10.18632/oncotarget.24990] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 11/25/2022] Open
Abstract
Identification of molecular targets and mechanism of action is always a challenge, in particular – for natural compounds due to inherent chemical complexity. BP-Cx-1 is a water-soluble modification of hydrolyzed lignin used as the platform for a portfolio of innovative pharmacological products aimed for therapy and supportive care of oncological patients. The present study describes a new approach, which combines in vitro screening of potential molecular targets for BP-Cx-1 using Diversity Profile - P9 panel by Eurofins Cerep (France) with a search of possible active components in silico in ChEMBL - manually curated chemical database of bioactive molecules with drug-like properties. The results of diversity assay demonstrate that BP-Cx-1 has multiple biological effects on neurotransmitters receptors, ligand-gated ion channels and transporters. Of particular importance is that the major part of identified molecular targets are involved in modulation of inflammation and immune response and might be related to tumorigenesis. Characterization of molecular composition of BP-Cx-1 with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and subsequent identification of possible active components by searching for molecular matches in silico in ChEMBL indicated polyphenolic components, nominally, flavonoids, sapogenins, phenanthrenes, as the major carriers of biological activity of BP-Cx-1. In vitro and in silico target screening yielded overlapping lists of proteins: adenosine receptors, dopamine receptor DRD4, glucocorticoid receptor, serotonin receptor 5-HT1, prostaglandin receptors, muscarinic cholinergic receptor, GABAA receptor. The pleiotropic molecular activities of polyphenolic components are beneficial in treatment of multifactorial disorders such as diseases associated with chronic inflammation and cancer.
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Affiliation(s)
- Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia.,Nobel LTD, Saint-Petersburg 192012, Russia
| | - Alexey A Orlov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Zherebker
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Ekaterina A Gubareva
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia
| | - Mikhail A Maydin
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia
| | | | - Konstantin A Krasnov
- Institute of Toxicology, Federal Medical-Biological Agency, Saint-Petersburg 192019, Russia
| | | | | | | | - Andrey V Panchenko
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia
| | - Margarita L Tyndyk
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia
| | - Dmitry I Osolodkin
- Institute of Poliomyelitis and Viral Encephalitides, Chumakov FSC R&D IBP RAS, Moscow 108819, Russia.,Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia.,Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119121, Russia
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir N Anisimov
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia
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27
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Vlaskin MS, Kostyukevich YI, Grigorenko AV, Kiseleva EA, Vladimirov GN, Yakovlev PV, Nikolaev EN. Hydrothermal treatment of organic waste. RUSS J APPL CHEM+ 2017. [DOI: 10.1134/s1070427217080158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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28
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Zhdanova E, Kostyukevich Y, Nikolaev E. Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:197-201. [PMID: 29028404 DOI: 10.1177/1469066717718369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Static harmonization in the Fourier transform ion cyclotron resonance cell improves the resolving power of the cell and prevents dephasing of the ion cloud in the case of any trajectory of the charged particle, not necessarily axisymmetric cyclotron (as opposed to dynamic harmonization). We reveal that the Fourier transform ion cyclotron resonance cell with dynamic harmonization (paracell) is proved to be statically harmonized. The volume of the statically harmonized potential distribution increases with an increase in the number of trap segments.
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Affiliation(s)
- Ekaterina Zhdanova
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Yury Kostyukevich
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Eugene Nikolaev
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
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