1
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Xiang Y, Yu Y, Wang J, Li W, Rong Y, Ling H, Chen Z, Qian Y, Han X, Sun J, Yang Y, Chen L, Zhao C, Li J, Chen K. Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171287. [PMID: 38423316 DOI: 10.1016/j.scitotenv.2024.171287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/24/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
It remains challenging to establish reliable links between transformation products (TPs) of contaminants and corresponding microbes. This challenge arises due to the sophisticated experimental regime required for TP discovery and the compositional nature of 16S rRNA gene amplicon sequencing and mass spectrometry datasets, which can potentially confound statistical inference. In this study, we present a new strategy by combining the use of 2H-labeled Stable Isotope-Assisted Metabolomics (2H-SIAM) with a neural network-based algorithm (i.e., MMvec) to explore links between TPs of pyrene and the soil microbiome. The links established by this novel strategy were further validated using different approaches. Briefly, a metagenomic study provided indirect evidence for the established links, while the identification of pyrene degraders from soils, and a DNA-based stable isotope probing (DNA-SIP) study offered direct evidence. The comparison among different approaches, including Pearson's and Spearman's correlations, further confirmed the superior performance of our strategy. In conclusion, we summarize the unique features of the combined use of 2H-SIAM and MMvec. This study not only addresses the challenges in linking TPs to microbes but also introduces an innovative and effective approach for such investigations. Environmental Implication: Taxonomically diverse bacteria performing successive metabolic steps of the contaminant were firstly depicted in the environmental matrix.
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Affiliation(s)
- Yuhui Xiang
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Yansong Yu
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jiahui Wang
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Weiwei Li
- Hubei Key Laboratory of Pollution Damage Assessment and Environmental Health Risk Prevention and Control, Hubei Provincial Academy of Eco-Environmental Sciences, Wuhan 430074, PR China
| | - Yu Rong
- Hubei Key Laboratory of Pollution Damage Assessment and Environmental Health Risk Prevention and Control, Hubei Provincial Academy of Eco-Environmental Sciences, Wuhan 430074, PR China
| | - Haibo Ling
- Hubei Key Laboratory of Pollution Damage Assessment and Environmental Health Risk Prevention and Control, Hubei Provincial Academy of Eco-Environmental Sciences, Wuhan 430074, PR China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha 16500, Czech Republic
| | - Yiguang Qian
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, PR China
| | - Xiaole Han
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jie Sun
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Liang Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Chao Zhao
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Juying Li
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China.
| | - Ke Chen
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China.
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2
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Maness P, McCulla RD. Insights into the Mechanism of O( 3P)-Mediated Oxidation of Alkenes through Kinetic Isotope Effects and Computational Modeling. J Org Chem 2024; 89:1458-1464. [PMID: 38262620 PMCID: PMC10846523 DOI: 10.1021/acs.joc.3c02075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024]
Abstract
Photodeoxygenation of aryl sulfoxides, such as dibenzothiophene S-oxide (DBTO), produces atomic oxygen [O(3P)] in solution. The mechanism of alkene oxidation with O(3P) remains uncertain. To address this, the current study utilized kinetic isotope effects (KIEs) and computational approaches to study the reaction of O(3P) with styrene and its isotopologues. Notably, the 2° CH/D KIE at the internal and terminal carbons of the reactive π-bond was ∼1.00 and ∼0.87, respectively. These findings indicate a terminal addition of O(3P) to the π-bond, supporting a stepwise oxidation pathway. Both epoxide and aldehyde products go through the same rate-determining transition state and then diverge based on the intermediate conformation. The O-C-C-C dihedral angle (φ) on the triplet surface dictates the product distribution, where φ = 50° or 310° leads to epoxide formation and φ = 180° leads to aldehyde formation. Computational modeling suggests that the epoxide is formed through rapid ring closure upon intersystem crossing from the triplet to the singlet ground state. Similarly, the aldehyde is generated via a 1,2-H shift immediately following intersystem crossing. This study integrates experimental and computational methods to understand the O(3P)-mediated oxidation of alkenes, providing supporting evidence for a stepwise addition mechanism.
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Affiliation(s)
- Peter
F. Maness
- Department of Chemistry, Saint Louis University, 2501 Laclede Avenue, St.
Louis, Missouri 63108, United States
| | - Ryan D. McCulla
- Department of Chemistry, Saint Louis University, 2501 Laclede Avenue, St.
Louis, Missouri 63108, United States
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3
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Yasui K. Production of O Radicals from Cavitation Bubbles under Ultrasound. Molecules 2022; 27:4788. [PMID: 35897962 PMCID: PMC9369501 DOI: 10.3390/molecules27154788] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
In the present review, the production of O radicals (oxygen atoms) in acoustic cavitation is focused. According to numerical simulations of chemical reactions inside a bubble using an ODE model which has been validated through studies of single-bubble sonochemistry, not only OH radicals but also appreciable amounts of O radicals are generated inside a heated bubble at the violent collapse by thermal dissociation of water vapor and oxygen molecules. The main oxidant created inside an air bubble is O radicals when the bubble temperature is above about 6500 K for a gaseous bubble. However, the concentration and lifetime of O radicals in the liquid water around the cavitation bubbles are unknown at present. Whether O radicals play some role in sonochemical reactions in the liquid phase, which are usually thought to be dominated by OH radicals and H2O2, should be studied in the future.
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Affiliation(s)
- Kyuichi Yasui
- National Institute of Advanced Industrial Science and Technology (AIST), Nagoya 463-8560, Japan
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4
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Borissov A, Maurya YK, Moshniaha L, Wong WS, Żyła-Karwowska M, Stępień M. Recent Advances in Heterocyclic Nanographenes and Other Polycyclic Heteroaromatic Compounds. Chem Rev 2022; 122:565-788. [PMID: 34850633 PMCID: PMC8759089 DOI: 10.1021/acs.chemrev.1c00449] [Citation(s) in RCA: 224] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 12/21/2022]
Abstract
This review surveys recent progress in the chemistry of polycyclic heteroaromatic molecules with a focus on structural diversity and synthetic methodology. The article covers literature published during the period of 2016-2020, providing an update to our first review of this topic (Chem. Rev. 2017, 117 (4), 3479-3716).
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Affiliation(s)
| | | | | | | | | | - Marcin Stępień
- Wydział Chemii, Uniwersytet
Wrocławski, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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5
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Reid AG, Moreno JJ, Hooe SL, Baugh KR, Thomas IH, Dickie DA, Machan CW. Inverse Potential Scaling in Co-Electrocatalytic Activity for CO 2 Reduction Through Redox Mediator Tuning and Catalyst Design. Chem Sci 2022; 13:9595-9606. [PMID: 36091894 PMCID: PMC9400620 DOI: 10.1039/d2sc03258a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrocatalytic CO2 reduction is an attractive strategy to mitigate the continuous rise in atmospheric CO2 concentrations and generate value-added chemical products. A possible strategy to increase the activity of molecular...
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Affiliation(s)
- Amelia G Reid
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Juan J Moreno
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Shelby L Hooe
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Kira R Baugh
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Isobel H Thomas
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Diane A Dickie
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Charles W Machan
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
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6
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Isor A, O'Dea AT, Grady SF, Petroff JT, Skubic KN, Aziz B, Arnatt CK, McCulla RD. Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O( 3P)-precursors. Photochem Photobiol Sci 2021; 20:1621-1633. [PMID: 34822125 DOI: 10.1007/s43630-021-00136-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
Photodeoxygenation of dibenzothiophene S-oxide and its derivatives have been used to generate atomic oxygen [O(3P)] to examine its effect on proteins, nucleic acids, and lipids. The unique reactivity and selectivity of O(3P) have shown distinct oxidation products and outcomes in biomolecules and cell-based studies. To understand the scope of its global impact on the cell, we treated MDA-MB-231 cells with 2,8-diacetoxymethyldibenzothiophene S-oxide and UV-A light to produce O(3P) without targeting a specific cell organelle. Cellular responses to O(3P)-release were analyzed using cell viability and cell cycle phase determination assays. Cell death was observed when cells were treated with higher concentrations of sulfoxides and UV-A light. However, significant differences in cell cycle phases due to UV-A irradiation of the sulfoxide were not observed. We further performed RNA-Seq analysis to study the underlying biological processes at play, and while UV-irradiation itself influenced gene expression, there were 9 upregulated and 8 downregulated genes that could be attributed to photodeoxygenation.
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Affiliation(s)
- Ankita Isor
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Austin T O'Dea
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Scott F Grady
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - John T Petroff
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Kristin N Skubic
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Bashar Aziz
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Christopher K Arnatt
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA
| | - Ryan D McCulla
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO, 63103, USA.
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7
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Rashid M, Baker DD, Greer A. Two-step Two-intermediate Photorelease Bolm-McCulla Reaction: Dual Release of Nitrene and Atomic Oxygen Reactive Intermediates. Photochem Photobiol 2021; 97:1453-1455. [PMID: 34242417 DOI: 10.1111/php.13485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022]
Abstract
This article is a highlight of the paper by Isor et al. in this issue of Photochemistry and Photobiology. It describes the photolysis of a dibenzothiophene sulfoximine (bearing N-phenyl imino and S-oxide groups) to produce two reactive intermediates in tandem. The sulfoximine undergoes a S-N and S-O photocleavage to release phenyl nitrene and atomic oxygen [O(3 P)]. The phenyl nitrene dimerizes to azobenzene or is trapped by diethylamine to reach an azepine. From there, atomic oxygen arises in a secondary photolysis of dibenzothiophene sulfoxide. A computational analysis also reveals that the S-N bond is labile for initial nitrene release, with the secondary release of atomic oxygen by S-O cleavage. Whether future sulfoximine scaffolds can produce the reverse order release of O(3 P) then nitrene, or release both simultaneously, is yet to be established. Nonetheless, molecules with dual-intermediate release, such as coupled photoaffinity labeling and cellular oxidation, are worth pursuing.
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Affiliation(s)
- Mahir Rashid
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY
| | - Devora D Baker
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY
| | - Alexander Greer
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY
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8
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Isor A, Hommelsheim R, Cone GW, Frings M, Petroff JT, Bolm C, McCulla RD. Photochemistry of N-Phenyl Dibenzothiophene Sulfoximine †. Photochem Photobiol 2021; 97:1322-1334. [PMID: 34022069 DOI: 10.1111/php.13456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 01/04/2023]
Abstract
Sulfoximines are popular scaffolds in drug discovery due to their hydrogen bonding properties and chemical stability. In recent years, the role of reactive intermediates such as nitrenes has been studied in the synthesis and degradation of sulfoximines. In this work, the photochemistry of N-phenyl dibenzothiophene sulfoximine [5-(phenylimino)-5H-5λ4 -dibenzo[b,d]thiophene S-oxide] was analyzed. The structure resembles a combination of N-phenyl iminodibenzothiophene and dibenzothiophene S-oxide, which generate nitrene and O(3 P) upon UV-A irradiation, respectively. The photochemistry of N-phenyl dibenzothiophene sulfoximine was explored by monitoring the formation of azobenzene, a photoproduct of triplet nitrene, using direct irradiation and sensitized experiments. The reactivity profile was further studied through direct irradiation experiments in the presence of diethylamine (DEA) as a nucleophile. The studies demonstrated that N-phenyl dibenzothiophene sulfoximine underwent S-N photocleavage to release singlet phenyl nitrene which formed a mixture of azepines in the presence of DEA and generated moderate amounts of azobenzene in the absence of DEA to indicate formation of triplet phenyl nitrene.
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Affiliation(s)
- Ankita Isor
- Department of Chemistry, Saint Louis University, St. Louis, MO
| | - Renè Hommelsheim
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Grant W Cone
- Department of Chemistry, Saint Louis University, St. Louis, MO
| | - Marcus Frings
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - John T Petroff
- Department of Chemistry, Saint Louis University, St. Louis, MO
| | - Carsten Bolm
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Ryan D McCulla
- Department of Chemistry, Saint Louis University, St. Louis, MO
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9
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Isor A, Chartier BV, Abo M, Currens ER, Weerapana E, McCulla RD. Identifying cysteine residues susceptible to oxidation by photoactivatable atomic oxygen precursors using a proteome-wide analysis. RSC Chem Biol 2021; 2:577-591. [PMID: 34458801 PMCID: PMC8341131 DOI: 10.1039/d0cb00200c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/03/2021] [Indexed: 12/18/2022] Open
Abstract
The reactivity profile of atomic oxygen [O(3P)] in the condensed phase has shown a preference for the thiol group of cysteines. In this work, water-soluble O(3P)-precursors were synthesized by adding aromatic burdens and water-soluble sulphonic acid groups to the core structure of dibenzothiophene-S-oxide (DBTO) to study O(3P) reactivity in cell lysates and live cells. The photodeoxygenation of these compounds was investigated using common intermediates, which revealed that an increase in aromatic burdens to the DBTO core structure decreases the total oxidation yield due to competitive photodeoxygenation mechanisms. These derivatives were then tested in cell lysates and live cells to profile changes in cysteine reactivity using the isoTOP-ABPP chemoproteomics platform. The results from this analysis indicated that O(3P) significantly affects cysteine reactivity in the cell. Additionally, O(3P) was found to oxidize cysteines within peptide sequences with leucine and serine conserved at the sites surrounding the oxidized cysteine. O(3P) was also found to least likely oxidize cysteines among membrane proteins.
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Affiliation(s)
- Ankita Isor
- Department of Chemistry, Saint Louis University 3501 Laclede Ave Saint Louis MO 63103 USA
| | | | - Masahiro Abo
- Department of Chemistry, Boston College Chestnut Hill MA 02467 USA
| | - Emily R Currens
- Department of Chemistry, Saint Louis University 3501 Laclede Ave Saint Louis MO 63103 USA
| | | | - Ryan D McCulla
- Department of Chemistry, Saint Louis University 3501 Laclede Ave Saint Louis MO 63103 USA
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10
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Chintala S, Maness PF, Petroff JT, Throgmorton JC, Zhang M, Omlid SM, McCulla RD. Photo-oxidation and Thermal Oxidations of Triptycene Thiols by Aryl Chalcogen Oxides. ACS OMEGA 2020; 5:32349-32356. [PMID: 33376871 PMCID: PMC7758903 DOI: 10.1021/acsomega.0c04293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Oxidation of thiols yield sulfenic acids, which are very unstable intermediates. As sulfenic acids are reactive, they form disulfides in the presence of thiols. However, sulfenic acids also oxidize to sulfinic acids (-SO2H) and sulfonic acids (-SO3H) at higher concentrations of oxidants. Hydrogen peroxide is a commonly used oxidant for the oxidation of thiols to yield sulfenic acids. However, hydrogen peroxide also oxidizes other reactive functional groups present in a molecule. In this work, the reaction intermediates arising from the oxidation of sterically hindered thiols by aryl chalcogen oxides, dibenzothiophene S-oxide (DBTO), dibenzoselenophene Se-oxide (DBSeO), and dibenzotellurophene Te-oxide (DBTeO), were investigated. Photodeoxygenation of DBTO produces triplet atomic oxygen [O(3P)], which has previously shown to preferentially react with thiols over other functional groups. Similarly, aryl selenoxides have also shown that they can thermally react selectively with thiols at room temperature to yield disulfides. Conversely, aryl telluroxides have been reported to oxidize thiols to disulfides thermally with no selectivity toward thiols. The results from this study demonstrate that sulfenic acids are an intermediate in the oxidation of thiols by DBTeO and by photodeoxygenation of DBTO. The results also showed that the oxidation of thiols by DBSeO yields sulfonic acids. Triptycene-9-thiol and 9-fluorotriptycene-10-thiol were for the thiols used in this oxidation reaction. This work expands the list of oxidants that can be used to oxidize thiols to obtain sulfenic acids.
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11
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Chintala SM, Throgmorton JC, Maness PF, McCulla RD. Visible light‐induced photodeoxygenation of polycyclic selenophene
Se
‐oxides. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Peter F. Maness
- Department of Chemistry Saint Louis University St. Louis MO USA
| | - Ryan D. McCulla
- Department of Chemistry Saint Louis University St. Louis MO USA
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12
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Nguyen TB. Recent Advances in the Synthesis of Heterocycles via Reactions Involving Elemental Sulfur. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000535] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Thanh Binh Nguyen
- Institut de Chimie des Substances NaturellesCNRS UPR 2301Université Paris-SudUniversité Paris-Saclay 1, avenue de la Terrasse Gif-sur-Yvette 91198 France
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