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Cai S, Zhang X, Chen S, Peng S, Sun T, Zhang Y, Yang P, Chai H, Wang D, Zhang W. Solid-liquid redistribution and degradation of antibiotics during hydrothermal treatment of sewage sludge: Interaction between biopolymers and antibiotics. WATER RESEARCH 2024; 258:121759. [PMID: 38754299 DOI: 10.1016/j.watres.2024.121759] [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: 02/02/2024] [Revised: 04/24/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Waste activated sludge serves an important reservoir for antibiotics within wastewater treatment plants, and understanding the occurrence and evolution of antibiotics during sludge treatment is crucial to mitigate the potential risks of subsequent resource utilization of sludge. This study explores the degradation and transformation mechanisms of three typical antibiotics, oxytetracycline (OTC), ofloxacin (OFL), and azithromycin (AZI) during sludge hydrothermal treatment (HT), and investigates the influence of biopolymers transformation on the fate of these antibiotics. The findings indicate that HT induces a shift of antibiotics from solid-phase adsorption to liquid-phase dissolution in the initial temperature range of 25-90 °C, underscoring this phase's critical role in preparing antibiotics for subsequent degradation phases. Proteins (PN) and humic acids emerge as crucial for antibiotic binding, facilitating their redistribution within sludge. Specifically, the binding capacity sequence of biopolymers to antibiotics is as follows: OFL>OTC>AZI, highlighting that OFL-biopolymers display stronger electrostatic attraction, more available adsorption sites, and more stable binding strength. Furthermore, antibiotic degradation mainly occurs above 90 °C, with AZI being the most temperature-sensitive, degrading 92.97% at 180 °C, followed by OTC (91.26%) and OFL (52.51%). Concurrently, the degradation products of biopolymers compete for active sites to form novel amino acid-antibiotic conjugates, which inhibits the further degradation of antibiotics. These findings illuminate the effects of biopolymers evolution on intricate dynamics of antibiotics fate in sludge HT and are helpful to optimize the sludge HT process for effective antibiotics abatement.
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Affiliation(s)
- Siying Cai
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Xinyu Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Shuaiyu Chen
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Sainan Peng
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Tong Sun
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Yu Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Peng Yang
- School of Civil Engineering and Architecture, Northeast Electric Power University, Jilin 132012, Jilin, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Dongsheng Wang
- Department of environmental engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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2
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Wen J, Tang X, Wang M, Mu L, Hao W, Weng J, Gao Z, Hu X. Regulation and mechanism of pyrite and humic acid on the toxicity of arsenate in lettuce. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168980. [PMID: 38040366 DOI: 10.1016/j.scitotenv.2023.168980] [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: 09/16/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Pyrite and humic acid are common substances in nature, and the combined effects of pyrite and humic acid on arsenic phytotoxicity are more widespread in the actual environments than that of a single substance, but have received less attention. In this study, the interaction between pyrite and humic acid in arsenate solution was studied, and the effects of pyrite and humic acid on plant toxicity of arsenate were evaluated. The results showed that arsenate + pyrite + fulvic acid (V-PF) treatment immobilized more arsenic by forming chemical bonds such as AsS and Fe-As-O and reduced the migration of arsenic to plants. Compared to the arsenate + fulvic acid (VF), arsenate + pyrite (VP) and arsenate (V) group, the inorganic arsenic content of lettuce leaves in the V- PF group was reduced by 19.8 %, 13.4 % and 13.4 %, respectively. In addition, the V-PF group increased the absorption of Ca, Fe and Cu in plant roots, and improved the activity of superoxide dismutase (SOD) in plant leaves. Compared to the VF group, SOD and MDA in the V-PF group increased by 34.1 % in 30 days and decreased by 47.3 % in 40 days, respectively. The biomass of lettuce in V-PF group was increased by 29.3 % compared with that in VF group on day 50. The protein content of the V-PF group was 58.3 % higher than that of the VF group and 23.1 % higher than that of the VP group. Furthermore, metabolomics analysis showed that the V-PF group promoted glycolysis by up-regulating glyoxylic acid and dicarboxylic acid metabolism, thus reducing carbohydrate accumulation. Phosphocreatine metabolism was also up-regulated, which decreased the oxidative damage in lettuce induced by arsenic. This study will provide new ideas for scientifically and rationally assessing the ecological environmental risks of arsenic and regulating its toxicity.
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Affiliation(s)
- Jingyu Wen
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Xin Tang
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Mengyuan Wang
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China.
| | - Weidan Hao
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China
| | - Jingxian Weng
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Ziwei Gao
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China
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3
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Xue Q, Jiao Z, Liu X, Pan W, Fu J, Zhang A. Dynamic Behavior and Interaction Mechanism of Soil Organic Matter in Water Systems: A Coarse-Grained Molecular Dynamics Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1531-1540. [PMID: 38118063 DOI: 10.1021/acs.est.3c05966] [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: 12/22/2023]
Abstract
Investigating soil organic matter's (SOM) microscale assembly and functionality is challenging due to its complexity. This study constructs comparatively realistic SOM models, including diverse components such as Leonardite humic acid (LHA), lipids, peptides, carbohydrates, and lignin, to unveil their spontaneous self-assembly behavior at the mesoscopic scale through microsecond coarse-grained molecular dynamics simulations. We discovered an ordered SOM aggregation creating a layered phase from its hydrophobic core to the aqueous phase, resulting in an increasing O/C ratio and declining structural amphiphilicity. Notably, the amphiphilic lipids formed a bilayer membrane, partnering with lignin to constitute SOM's hydrophobic core. LHA, despite forming a layer, was embedded within this structure. The formation of such complex architectures was driven by nonbonded interactions between components. Our analysis revealed component-dependent diffusion effects within the SOM system. Lipids, peptides, and lignin showed inhibitory effects on self-diffusion, while carbohydrates facilitated diffusion. This study offers novel insights into the dynamic behavior and assembly of SOM components, introducing an effective approach for studying dynamic SOM mechanisms in aquatic environments.
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Affiliation(s)
- Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Zhiyue Jiao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, P. R. China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, P. R. China
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Zhou Z, Zhang C, Xi M, Ma H, Jia H. Multi-scale modeling of natural organic matter-heavy metal cations interactions: Aggregation and stabilization mechanisms. WATER RESEARCH 2023; 238:120007. [PMID: 37121201 DOI: 10.1016/j.watres.2023.120007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/17/2023]
Abstract
Interaction between natural organic matters (NOM) and heavy metal cations in aqueous environment are of great significance for maintaining stability of organic carbon and restraining transport of heavy metal contaminants in (bio)geochemical processes. We systematically explore the aggregation process and complexation between NOM and heavy metal cations (Ag+, Cd2+, Pb2+, Zn2+, Eu3+) under different pH condition by molecular dynamics (MD) simulations, umbrella sampling method, and quantum chemistry calculations. The character of molecular structures NOM-heavy metal complexes and association are quantified. In acidic pH condition, aggregation proceeds via H-bonding and π-π interactions between NOM fragments. In neutral condition, Ag+, Cd2+, Pb2+, and Eu3+ can form inner-sphere complexes with the surface carboxylic groups and therefore reduce intermolecular charge repulsion, eventually leading to NOM aggregation, and it shows that even without direct binding, the outer-sphere adsorbed Zn2+ can also result in the formation of NOM assemble through H-bonding. Consequently, these heavy metals are capable of promoting NOM aggregation regardless of the complexing ways. Complexing free energy calculations characterized the dynamic processes of cations binding to the carboxylic groups of NOM fragment and the related energy landscape. This study provides quantitative insights for understanding the environmental processes of heavy metals and cycle of C in aquatic ecosystem, and contributes to developing environment-friendly strategies for controlling heavy metal contaminants.
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Affiliation(s)
- Zhiyu Zhou
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China
| | - Chi Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China; Key Laboratory of Low-Carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi, 712100, P.R. China.
| | - Mengning Xi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China
| | - Haonan Ma
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China; Key Laboratory of Low-Carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi, 712100, P.R. China.
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5
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Andrejiová A, Adamec S, Hegedűsová A, Hegedűs O, Rosa R. Verification of the humic substances and PGPB biostimulants beneficial effects on the potato yield and bioactive substances content. POTRAVINARSTVO 2023. [DOI: 10.5219/1805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Potatoes are one of the most important sources of nutrients worldwide, but excessive doses of industrial fertilizers are usually used to achieve higher yields. Soil biostimulants are an increasingly used alternative for reducing fertilizer doses and growing healthy agricultural products. In this study, we examined the effects of humic substances (Agriful) and beneficial bacteria (Groundfix) based biostimulants applied by dripping irrigation on the yield and quality of potato tubers in comparison with the conventional N fertilization system. The small trail field experiment was founded in the growing season of 2020 in the Botanical Garden of the Slovak University of Agriculture in Nitra. The highest tubers yield had the combination of biostimulants and N fertilizer – 195.16% above to control. Simultaneously this combination reached an increase in refractometric dry matter content, starch content – 3.6%, and vitamin C content – 20% increase above to control. The Groundfix variant had the highest antioxidant activity with a 16.2% difference compared to the conventional nitrogen fertilization variant. These results show the positive effect of applied biostimulants on the yield and quality of cultivated potatoes.
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6
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Socol DC. Clinical review of humic acid as an antiviral: Leadup to translational applications in clinical humeomics. Front Pharmacol 2023; 13:1018904. [PMID: 36712657 PMCID: PMC9875298 DOI: 10.3389/fphar.2022.1018904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
This clinical review presents what is known about the antiviral features of humic substances (HS) to the benefit of the clinical healthcare provider using available data in humeomics, the study of the soil humeome. It provides the reader with a working framework of historical studies and includes clinically relevant data with the goal of providing a broad appreciation of the antiviral potential of humic substances while also preparing for a translational leap into the clinical application of humic acid.
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Affiliation(s)
- David C. Socol
- Advanced Humeomics LLC, Beverly Hills, CA, United States
- SocolMD, Beverly Hills, CA, United States
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7
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Zhao N, Ju F, Song Q, Qi Z, Ling H. Quantitative assessment of the contribution of soil organic matter functional groups and heteroatoms to PAHs adsorption based on the COSMO-RS model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157415. [PMID: 35850341 DOI: 10.1016/j.scitotenv.2022.157415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/30/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Soil organic matter (SOM) is considered as a pivotal factor influencing the adsorption of pollutants. However, few prior quantitative investigations of the SOM functional group distribution to the contaminants' fate have been conducted. In this paper, the SOM cluster method based on COSMO-RS theory has been conducted to illustrate the chemical composition variables of SOM that affect the polycyclic aromatic hydrocarbons (PAHs) fate in quantitative terms. In the theoretical simulations, the contributions of carbonyl, carboxyl, aromatic, oxyalkyl and aliphatic groups in SOM to phenanthrene (Phe) and pyrene (Pyr) adsorption are evaluated by calculating the partition coefficients (LogP). The results show that the increase in oxyalkyl content leads to a decrease in LogP. Inversely, carbonyl and carboxyl groups of SOMs positively associated with Phe adsorption. The changes in aromatic and alkyl components have a similar magnitude of influence on LogP. Moreover, the effect of non-carbon-based functional groups in SOM on the Phe partitioning has been examined for the first time. The increase of sulfur and nitrogen content in SOM hinder Phe adsorption, while the rise of phosphorus content promotes the adsorption. In soil adsorption experiments, four natural soils, characterized by X-ray photoelectron spectroscopy (XPS) and Diffuse reflectance infrared Fourier transform (DRIFT), are selected to verify the influence of SOM functional group distribution. Comparing the experimental SOM-water partition coefficient (LogKoc) with the simulation predicted LogP suggests that the COSMO-RS based SOM cluster method can predict PAHs adsorption ability in SOM.
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Affiliation(s)
- Nan Zhao
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Feng Ju
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China; Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht 3584CE, Netherlands
| | - Quanwei Song
- State Key Laboratory of Petroleum Pollution Control, Beijing 102206, China; CNPC Research Institute of Safety and Environmental Technology, Beijing 102206, China
| | - Zhiwen Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Ling
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Scott SE, Fernandez JP, Hadad CM, MacKay AA. Molecular Docking as a Tool to Examine Organic Cation Sorption to Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:951-961. [PMID: 35038871 DOI: 10.1021/acs.est.1c06147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular docking simulations were performed to examine the structural effects of organic cations on their sorption to organic matter. A set of benzylamine compounds was used to assess the sorption trends arising from the systematic structural differences between ring or nitrogen substituents. Binding simulations were performed using AutoDock 4.2 with Schulten's proposed soil organic matter as a representative organic matter structure. The calculated binding energies for the sorbate compounds correlated strongly with the measured sorption energies for Pahokee peat, indicating that the simulated binding energies and their associated sorbate orientations were representative of the experimental conditions. Graphical docking orientations showed primary, secondary, and tertiary aminium compounds to form hydrogen-bond interactions with deprotonated carboxylic acid groups in a pocket of the organic matter structure. Quaternary ammonium compounds formed pi-pi or cation-pi interactions with the aromatic groups elsewhere in the same organic matter pocket. Ring substituents showed no clear trends in sorption energies with the substituent group type for primary aminium compounds. Rather, substituent groups altered the simulated van der Waals, electrostatic, hydrogen-bond, and desolvation energy contributions to the overall sorption energies, in part because of the variations in docking orientations between compounds. Increasing methyl substitution of the aminium nitrogen group was associated with an increase in van der Waals energy contributions and a decrease in electrostatic energy contributions to the overall compound sorption energies because of aminium charge delocalization into methyl substituents and steric hindrance from methyl substituents to form specific interactions. The findings illustrate how molecular docking can be used to explore the effects of organic cation structure on sorption interactions with organic matter.
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Affiliation(s)
- Sharon E Scott
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Joseph P Fernandez
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Allison A MacKay
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43210, United States
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Eswaran SV. Value-Added Products From Soil, Brown Coal, and Composted City Solid Waste. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.738899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This review article highlights alternative innovative uses of soil, brown coal, and composted solid city waste. The latter leads to environmental pollution, which can be addressed by using these materials to generate value-added products. Humic substances present there can be isolated in large amounts and used in diverse fields like sustainable agriculture, horticulture, biomedicine, and materials science. These have been shown to be non-toxic and safe for humans and serve as growth promotants for plants and to cure stomach ailments. The recent discovery of their antiviral/anti-HIV-AIDS activity is described here in some detail. The use of humic substances for making dye-sensitized solar cells (DSSCs) and for preparing a catalyst for reduction and for oxidation processes is also highlighted. Such innovative uses of humic substances can lead to environmental cleaning and positively impact climate change.
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López-Martínez VG, Guerrero-Álvarez JA, Ronderos-Lara JG, Murillo-Tovar MA, Solá-Pérez JE, León-Rivera I, Saldarriaga-Noreña H. Spectral Characteristics Related to Chemical Substructures and Structures Indicative of Organic Precursors from Fulvic Acids in Sediments by NMR and HPLC-ESI-MS. Molecules 2021; 26:molecules26134051. [PMID: 34279390 PMCID: PMC8272027 DOI: 10.3390/molecules26134051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to determine Fulvic Acids (FAs) in sediments to better know their composition at the molecular level and to propose substructures and structures of organic precursors. The sediment samples were obtained from a priority area for the conservation of ecosystems and biodiversity in Mexico. FAs were extracted and purified using modifications to the International Humic Substances Society method. The characterization was carried out by 1D and 2D nuclear magnetic resonance (NMR) and high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) in positive (ESI+) and negative (ESI−) modes. Twelve substructures were proposed by the COSY and HSQC experiments, correlating with compounds likely belonging to lignin derivatives obtained from soils as previously reported. The analysis of spectra obtained by HPLC-ESI-MS indicated likely presence of compounds chemically similar to that of the substructures elucidated by NMR. FAs studied are mainly constituted by carboxylic acids, hydroxyl, esters, vinyls, aliphatics, substituted aromatic rings, and amines, presenting structures related to organic precursors, such as lignin derivatives and polysaccharides.
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Affiliation(s)
- Verónica Gisela López-Martínez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Jorge A. Guerrero-Álvarez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - José Gustavo Ronderos-Lara
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Mario Alfonso Murillo-Tovar
- CONACYT-Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62290, Morelos, Mexico;
| | - Jorge Ernesto Solá-Pérez
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburna de Hidalgo Inn, Merida C.P. 97203, Yucatán, Mexico;
| | - Ismael León-Rivera
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Hugo Saldarriaga-Noreña
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
- Correspondence:
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11
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Gotsmy M, Escalona Y, Oostenbrink C, Petrov D. Exploring the structure and dynamics of proteins in soil organic matter. Proteins 2021; 89:925-936. [PMID: 33675059 PMCID: PMC8360018 DOI: 10.1002/prot.26070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/27/2021] [Accepted: 02/23/2021] [Indexed: 01/17/2023]
Abstract
Alongside inorganic materials, water, and air, soil organic matter (SOM) is one of the major components of soil and has tremendous influence on the environment given its vital role in the carbon cycle. Many soil dwelling organisms like plants, fungi and bacteria excrete proteins, whose interaction with SOM is poorly understood on an atomistic level. In this study, molecular dynamics simulations were used to investigate selected proteins in soil models of different complexity from simple co-solvent molecules to Leonardite humic acids (LHA). We analyzed the proteins in terms of their structural stability, the nature and strength of the interactions with their surroundings, as well as their aggregation behavior. Upon insertion of proteins in complex SOM models, their structural stability decreased, although no unfolding or disruption of secondary structure was observed. The interactions of proteins and SOM were primarily governed by electrostatic forces, often in form of hydrogen bonds. However, also weaker van der Waals forces made a significant contribution to the total interaction energies. Moreover, we showed that even though the molecular structure and size of SOM molecules varied, the functional groups of SOM ordered around the protein in a similar pattern. Finally, the number of aggregates formed by proteins and SOM molecules was shown to be primarily proportional to the size of the latter. Strikingly, for varying protein net charges no changes in the formation of aggregates with the strongly negatively charged LHA were observed.
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Affiliation(s)
- Mathias Gotsmy
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Yerko Escalona
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Drazen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
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Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis. Molecules 2021; 26:molecules26040782. [PMID: 33546346 PMCID: PMC7913487 DOI: 10.3390/molecules26040782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/24/2021] [Accepted: 01/29/2021] [Indexed: 11/16/2022] Open
Abstract
Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.
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Guo F, Zhou M, Xu J, Fein JB, Yu Q, Wang Y, Huang Q, Rong X. Glyphosate adsorption onto kaolinite and kaolinite-humic acid composites: Experimental and molecular dynamics studies. CHEMOSPHERE 2021; 263:127979. [PMID: 32841877 DOI: 10.1016/j.chemosphere.2020.127979] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
Glyphosate (PMG) has been the most widely used herbicide in the world, and its environmental mobility and fate are mainly controlled by interactions with mineral surfaces. In soil systems, kaolinite is typically associated with humic acids (HAs) in the form of mineral-HA complexes, and hence it is crucial to characterize the molecular-scale interactions that occur between PMG and kaolinite and kaolinite-HA complexes. Batch experiments, Fourier transform infrared spectrum (FTIR) and X-ray photoelectron spectroscopy (XPS), isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations were performed to decipher the molecular interactions between PMG and kaolinite and kaolinite-HA composites. Our results reveal that kaolinite-HA composites adsorb higher concentrations of PMG than does kaolinite alone, likely due to more adsorption sites existed on kaolinite-HA than on kaolinite. FTIR and XPS analysis reveal that the carboxyl, phosphonyl and amino groups of PMG interacted with kaolinite and kaolinite-humic acid via Hydrogen bonds. The ITC results and interaction energy calculations indicate that the adsorption of PMG onto the kaolinite-HA is more energetically favorable relative to that onto kaolinite. MD simulations suggest that the PMG molecule adsorbs parallel to the surface of kaolinite and the composites through hydrogen bonding. Humic acid increases the adsorption of PMG through the creation of H-bond networks between PMG, the kaolinite surface, and humic acid. The results from this study improve our molecular-level understanding of the interactions between PMG and two important components of soil systems, and hence yield valuable information for characterizing the fate and behavior of PMG in soil environments.
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Affiliation(s)
- Fayang Guo
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Zhou
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingcheng Xu
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jun Gong Road, Shanghai, 200093, PR China
| | - Jeremy B Fein
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Qiang Yu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Yingwei Wang
- School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, 221116, Jiangsu, China
| | - Qiaoyun Huang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingmin Rong
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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Vialykh EA, McKay G, Rosario-Ortiz FL. Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15904-15913. [PMID: 33269593 DOI: 10.1021/acs.est.0c05860] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.
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Affiliation(s)
- Elena A Vialykh
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Garrett McKay
- Zachry Department of Civil & Environmental Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Fernando L Rosario-Ortiz
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Environmental Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309, United States
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15
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Cha JY, Kang SH, Ali I, Lee SC, Ji MG, Jeong SY, Shin GI, Kim MG, Jeon JR, Kim WY. Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis. Sci Rep 2020; 10:15042. [PMID: 32929162 PMCID: PMC7490348 DOI: 10.1038/s41598-020-71701-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Imdad Ali
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sang Cheol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, PMBBRC, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jong-Rok Jeon
- Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea.
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Molecular dynamics simulation of homology modeled glomalin related soil protein (Rhizophagus irregularis) complexed with soil organic matter model. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00590-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Petrov D, Tunega D, Gerzabek MH, Oostenbrink C. Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid. EUROPEAN JOURNAL OF SOIL SCIENCE 2020; 71:831-844. [PMID: 33041627 PMCID: PMC7540484 DOI: 10.1111/ejss.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 05/08/2023]
Abstract
Soil organic matter (SOM) is abundant in the environment and plays an important role in several biogeochemical processes, including microbial activity, soil aggregation, plant growth and carbon storage. One of its key functions is the retention and release of various chemical compounds, primarily governed by the sorption process, which strongly affects the environmental fate of nutrients and pollutants. Sorption largely depends on the composition of SOM, as well as its structure, dynamics and the thermodynamic conditions. Although several approaches are available, experimental characterization of sorption mechanisms is not easy. Computational models for predicting sorption coefficients often require a wealth of experimental data for training and are only applicable to compounds and conditions related to the training dataset. Here, we use molecular dynamics (MD) simulations to study the sorption of a range of small organic compounds. As a model SOM system we use the standard Leonardite humic acid (LHA) sample, which physicochemical properties have recently been characterized computationally in detail. This model allowed us to estimate sorption propensities of the systems at two different hydration levels (water activities close to 0 and 1), showing a remarkable correlation with experimental data. Importantly, this molecular modelling approach based on perturbation free-energy calculations is rigorously derived from statistical thermodynamics and requires no experimental sorption data for training. It is therefore in principle applicable to any SOM model or thermodynamic condition. Moreover, the power of MD simulations to provide high-resolution insight into atomistic and molecular interactions was employed to explore how sorbate molecules associate with the LHA matrix and which contacts they form. The heteroatoms of both sorbate and sorbent play an important role and water molecules are identified as further key players in facilitating the sorption process. HIGHLIGHTS Modelling of the sorption processes in soil organic matter at atomistic level.Rigorous, physics-based approach applicable to a range of SOM systems and conditions.Remarkable level of matching with experimental data with additional insight into the molecular mechanism.Interactions between the sorbate and local environment strongly affects the sorption process.
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Affiliation(s)
- Drazen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Daniel Tunega
- Department of Forest and Soil SciencesInstitute of Soil Research, University of Natural Resources and Life Sciences ViennaViennaAustria
- School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinPeople's Republic of China
| | - Martin H. Gerzabek
- Department of Forest and Soil SciencesInstitute of Soil Research, University of Natural Resources and Life Sciences ViennaViennaAustria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
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18
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Wnuk E, Waśko A, Walkiewicz A, Bartmiński P, Bejger R, Mielnik L, Bieganowski A. The effects of humic substances on DNA isolation from soils. PeerJ 2020; 8:e9378. [PMID: 32775047 PMCID: PMC7384437 DOI: 10.7717/peerj.9378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background Humic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions. Methods The research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV-Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. Results Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
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Affiliation(s)
- Ewa Wnuk
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Adam Waśko
- Faculty of Food Science and Biotechnology, Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences, Lublin, Poland
| | - Anna Walkiewicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Piotr Bartmiński
- Department of Geology, Soil Science and Geoinformation, Maria Curie-Skłodowska University, Lublin, Poland
| | - Romualda Bejger
- Department of Bioengineering, West Pomeranian University of Technology, Szczecin, Poland
| | - Lilla Mielnik
- Department of Bioengineering, West Pomeranian University of Technology, Szczecin, Poland
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Zhao N, Ju F, Pan H, Tang Z, Ling H. Molecular dynamics simulation of the interaction of water and humic acid in the adsorption of polycyclic aromatic hydrocarbons. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:25754-25765. [PMID: 32350842 DOI: 10.1007/s11356-020-09018-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Humic acid (HA) and water play an important role in polycyclic aromatic hydrocarbons (PAHs) adsorption and biodegradation in soil. In this work, molecular dynamics (MD) and electrostatic potential surfaces (EPSs) simulations are conducted to research the contribution of quartz surface, leonardite humic acid (LHA), and water to PAH adsorption. The adsorption energies between PAHs and LHA are much higher than that between PAHs and quartz. Simulation shows that the hydroxyl and carboxyl groups' attraction by LHA is the main adsorption force between PAHs and LHA. The π-π interaction between PAHs and LHA also contributes to the adsorption process. In addition, the mobility of water on quartz surface is much higher than that of LHA. Water should be regarded as an adsorbate in the system as well as PAHs. However, the presence of water has a remarkable negative effect on the adsorption of PAHs on LHA and quartz. The bridging effect of water could only enhance the stability of the aggregation system. The adsorption contribution of quartz and LHA to PAHs in the soil model tends to 0 if the water layer reaches 2.0 nm. Graphical abstract.
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Affiliation(s)
- Nan Zhao
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Feng Ju
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui Pan
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhihe Tang
- Research Institute of Safety & Environment Technology, China National Petroleum Corporation, Beijing, 102206, China
| | - Hao Ling
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Sorption of Organic Pollutants by Humic Acids: A Review. Molecules 2020; 25:molecules25040918. [PMID: 32092867 PMCID: PMC7071110 DOI: 10.3390/molecules25040918] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 11/17/2022] Open
Abstract
Humic acids (HA) are promising green materials for water and wastewater treatment. They show a strong ability to sorb cationic and hydrophobic organic pollutants. Cationic compounds interact mainly by electrostatic interaction with the deprotonated carboxylic groups of HA. Other functional groups of HA such as quinones, may form covalent bonds with aromatic ammines or similar organic compounds. Computational and experimental works show that the interaction of HA with hydrophobic organics is mainly due to π-π interactions, hydrophobic effect and hydrogen bonding. Several works report that sorbing efficiency is related to the hydrophobicity of the sorbate. Papers about the interaction between organic pollutants and humic acids dissolved in solution, in the solid state and adsorbed onto solid particles, like aluminosilicates and magnetic materials, are reviewed and discussed. A short discussion of the thermodynamics and kinetics of the sorption process, with indication of the main mistakes reported in literature, is also given.
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Ai Y, Zhao C, Sun L, Wang X, Liang L. Coagulation mechanisms of humic acid in metal ions solution under different pH conditions: A molecular dynamics simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:135072. [PMID: 31731124 DOI: 10.1016/j.scitotenv.2019.135072] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Humic acid (HA) exerts a variety of significant environmental and geochemical influences on the soils, sediments and aqueous environments. The interaction with metal ions induces strong HA-metal complexation, thus effecting the transport of the toxic metals as well as the colloidal aggregation of HA. In the present work, we systematically report and analyze the aggregation mechanisms of HAs in solutions filled with different heavy cations (Ag+, Cd2+ and Cr3+) or common metal ions (Na+, Ca2+ and Al3+) under neutral and low pH conditions by using molecular dynamic simulations. We aim to explore the effects of pH, metal ions type and other possible weak interactions on the aggregation capabilities of HA. Scrutiny of the simulation results showed that the aggregation of HAs under neutral condition was driven by the HA-metal complexation which combined the effects of electrostatic attraction and inter-molecular bridging between cations and COO- groups. Larger extent of aggregation was found in heavy metal ions compared with the common ones. On the other hand, under low pH condition, due to the protonation states of carboxyl and phenolic group, the aggregation of HAs was stabilized mainly by weak forces, such as hydrogen bonds between different functional groups. In addition, other weak interactions such as the hydrophilic and hydrophobic effects, the cation-π interactions have also been proposed to be progressive effects on the coagulation behavior. Our computational studies give supplement to the experimental observation and provide insights into the intrinsic mechanisms of the aggregation behavior of HAs and their complexation with metal ions. Such computational modelling supplied a highly effective tool for qualitatively evaluating their roles in environmental remediation.
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Affiliation(s)
- Yuejie Ai
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, PR China
| | - Chaofeng Zhao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, PR China
| | - Lu Sun
- Institute of Modern Optics, Nankai University, Tianjin 300350, PR China.
| | - Xiangke Wang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, PR China
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou 310018, PR China
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Khil’ko SL, Rogatko MI, Makarova RA, Semenova RG. Tensiometric and Rheological Characteristics of Fractions of Humic and Hymatomelanic Acids. COLLOID JOURNAL 2020. [DOI: 10.1134/s1061933x2001007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Li M, Hu H, He X, Jia J, Drosos M, Wang G, Liu F, Hu Z, Xi B. Organic Carbon Sequestration in Soil Humic Substances As Affected by Application of Different Nitrogen Fertilizers in a Vegetable-Rotation Cropping System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3106-3113. [PMID: 30807137 DOI: 10.1021/acs.jafc.8b07114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Little is known on the effect of application of different nitrogen (N) fertilizers on soil organic carbon (SOC) sequestration in soil humic substances (HS). We investigated HS molecular characteristics in an Orthic Acrisol, southwestern China, under 2-year field fertilization of a urea (U), a polymer-coated urea (PCU) and a biochar-coated urea (BCU) using 13C-CPMAS-NMR spectroscopy. Results showed that N fertilization promoted SOC sequestration into HS and favored alkyl-C and aromatic-C rather than O-alkyl-C and carbonyl-C for humic acids and humin in soil. Application of PCU and BCU may better enhance vegetable yield, SOC sequestration, and HS stability than the U application, which may benefit from longer time of N existence and higher total N in soil. Among the N treatments, BCU application mostly affected the compositions and stability of SOC in the HS for the OC input and prime effect of biochar for SOC transformation.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing 100012 , China
- College of Resources and Environment, Sino-Danish College , University of Chinese Academy of Sciences , Beijing 100049 , China
- Department of Plant and Environmental Sciences, Crop Science Section , University of Copenhagen , Højbakkegaard Allé 13 , DK-2630 Taastrup , Denmark
| | - Hualing Hu
- College of Environmental Sciences and Engineering , Tianjin University , Tianjin 300035 , China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing 100012 , China
| | - Jinhu Jia
- China Environmental Science Press , Beijing 100062 , China
| | - Marios Drosos
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l'Ambiente, l'Agroalimentare ed i Nuovi Materiali (CERMANU) , Università di Napoli "Federico II" , via Università 100 , 80055 Portici , Italy
| | - Guoxi Wang
- College of Resources and Environment, Sino-Danish College , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Fulai Liu
- Department of Plant and Environmental Sciences, Crop Science Section , University of Copenhagen , Højbakkegaard Allé 13 , DK-2630 Taastrup , Denmark
| | - Zhengyi Hu
- College of Resources and Environment, Sino-Danish College , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing 100012 , China
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Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. J Comput Aided Mol Des 2018; 32:1259-1271. [DOI: 10.1007/s10822-018-0164-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022]
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25
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Effects of Oxidized Brown Coal Humic Acid Fertilizer on the Relative Height Growth Rate of Three Tree Species. FORESTS 2018. [DOI: 10.3390/f9060360] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Shah ZH, Rehman HM, Akhtar T, Alsamadany H, Hamooh BT, Mujtaba T, Daur I, Al Zahrani Y, Alzahrani HAS, Ali S, Yang SH, Chung G. Humic Substances: Determining Potential Molecular Regulatory Processes in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:263. [PMID: 29593751 PMCID: PMC5861677 DOI: 10.3389/fpls.2018.00263] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/14/2018] [Indexed: 05/20/2023]
Abstract
Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant's tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review.
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Affiliation(s)
- Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronics and Biomedical Engineering, Chonnam National University, Gwangju, South Korea
| | - Tasneem Akhtar
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hameed Alsamadany
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bahget T. Hamooh
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tahir Mujtaba
- Plant and Forest Biotechnology Umeå, Plant Science Centre, Swedish University of Agriculture Sciences, Umeå, Sweden
| | - Ihsanullah Daur
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yahya Al Zahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hind A. S. Alzahrani
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Shawkat Ali
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | - Seung H. Yang
- Department of Electronics and Biomedical Engineering, Chonnam National University, Gwangju, South Korea
| | - Gyuhwa Chung
- Department of Electronics and Biomedical Engineering, Chonnam National University, Gwangju, South Korea
- *Correspondence: Gyuhwa Chung,
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Petrov D, Tunega D, Gerzabek MH, Oostenbrink C. Molecular Dynamics Simulations of the Standard Leonardite Humic Acid: Microscopic Analysis of the Structure and Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5414-5424. [PMID: 28440077 DOI: 10.1021/acs.est.7b00266] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Humic substances (HS) are abundant in the environment and play an important role in a number of biogeochemical processes including microbial activity, soil aggregation, plant growth, the retention and release of nutrients, the environmental fate of pollutants, and carbon storage. They are flexible, relatively small molecules forming supramolecular structures through weak interactions. Despite the great importance of understanding their behavior at the atomic level, computational modeling, a premier high-resolution technique providing great level of detail, has been surprisingly little-employed to study humic substances. Here, we use the recently developed Vienna Soil Organic-Matter Modeler to create representative models of a real HS sample, the standard Leonardite humic acid. Molecular dynamics simulations were used to probe the structure and dynamics of the system at a range of hydration levels. The studied systems were characterized in terms of their physicochemical properties, including density, dielectric properties, hydrogen bonding, etc. Moreover, the strength of sorption was estimated for three small organic compounds: benzaldehyde, propan-2-ol, and acetone. Strikingly, the HS models were validated against experimental data showing a remarkable agreement with calculated properties. Finally, we make the equilibrated models of the standard Leonardite humic acid, together with corresponding force-field parameters, available at the Vienna Soil Organic-Matter Modeler.
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Affiliation(s)
- Drazen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria
| | - Daniel Tunega
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna , Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Martin H Gerzabek
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna , Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria
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Dror I, Yaron B, Berkowitz B. Microchemical contaminants as forming agents of anthropogenic soils. AMBIO 2017; 46:109-120. [PMID: 27344323 PMCID: PMC5226898 DOI: 10.1007/s13280-016-0804-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/01/2016] [Accepted: 06/11/2016] [Indexed: 05/12/2023]
Abstract
Within historically accepted, major soil-forming major processes, the role of chemicals as a human-induced factor was neglected until the middle of the last century. Over the years, however, anthropogenic chemicals have emerged and are being released on the land surface in large amounts. Irreversible changes in the matrix of soil and soil constituents may occur as a result of both intentional and accidental release of anthropogenic chemicals, as well as a byproduct of human activity. After presenting an historical evolution of the discussion on soil-forming factors, we focus here on human impacts and examine the abiotic role of anthropogenic microchemical contaminant (AMCC) interactions with soils at the molecular level. Selected examples of microchemical contaminants, including heavy metals, pesticides, hydrocarbons, and engineered nanomaterials, are presented to demonstrate that AMCCs-even at low concentration-may irreversibly alter the matrix of the soil and soil constituents and lead to the formation of anthropogenic soils with different properties than those of the pristine soils.
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Affiliation(s)
- Ishai Dror
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - Bruno Yaron
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Brian Berkowitz
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
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Sündermann A, Solc R, Tunega D, Haberhauer G, Gerzabek MH, Oostenbrink C. Vienna Soil-Organic-Matter Modeler—Generating condensed-phase models of humic substances. J Mol Graph Model 2015; 62:253-261. [DOI: 10.1016/j.jmgm.2015.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 11/29/2022]
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Mazzei P, Piccolo A. Interactions between natural organic matter and organic pollutants as revealed by NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:667-678. [PMID: 25783763 DOI: 10.1002/mrc.4209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Natural organic matter (NOM) plays a critical role in regulating the transport and the fate of organic contaminants in the environment. NMR spectroscopy is a powerful technique for the investigation of the sorption and binding mechanisms between NOM and pollutants, as well as their mutual chemical transformations. Despite NMR relatively low sensibility but due to its wide versatility to investigating samples in the liquid, gel, and solid phases, NMR application to environmental NOM-pollutants relations enables the achievement of specific and complementary molecular information. This report is a brief outline of the potentialities of the different NMR techniques and pulse sequences to elucidate the interactions between NOM and organic pollutants, with and without their labeling with nuclei that enhance NMR sensitivity.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
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