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Salahshoori I, Namayandeh Jorabchi M, Mazaheri A, Mirnezami SMS, Afshar M, Golriz M, Nobre MAL. Tackling antibiotic contaminations in wastewater with novel Modified-MOF nanostructures: A study of molecular simulations and DFT calculations. ENVIRONMENTAL RESEARCH 2024; 252:118856. [PMID: 38599447 DOI: 10.1016/j.envres.2024.118856] [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: 02/13/2024] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
The contamination of wastewater with antibiotics has emerged as a critical global challenge, with profound implications for environmental integrity and human well-being. Adsorption techniques have been meticulously investigated and developed to mitigate and alleviate their effects. In this study, we have investigated the adsorption behaviour of Erythromycin (ERY), Gentamicin (GEN), Levofloxacin (LEVO), and Metronidazole (MET) antibiotics as pharmaceutical contaminants (PHCs) on amide-functionalized (RC (=O)NH2)/MIL-53 (Al) (AMD/ML53A), using molecular simulations and density functional theory (DFT) calculations. Based on our DFT calculations, it becomes apparent that the adsorption tendencies of antibiotics are predominantly governed by the presence of AMD functional groups on the adsorbent surface. Specifically, hydrogen bonding (HB) and van der Waals (vdW) interactions between antibiotics and AMD groups serve as the primary mechanisms facilitating adsorption. Furthermore, we have observed that the adsorption behaviors of these antibiotics are influenced by their respective functional groups, molecular shapes, and sizes. Our molecular simulations delved into how the AMD/ML53A surfaces interact with antibiotics as PHCs. Moreover, various chemical quantum descriptors based on Frontier Molecular Orbitals (FMO) were explored to elucidate the extent of AMD/ML53A adsorption and to assess potential alterations in their electronic properties throughout the adsorption process. Monte Carlo simulation showed that ERY molecules adsorb stronger to the adsorbent in acidic and basic conditions than other contaminants, with high energies: -404.47 kcal/mol in acidic and -6375.26 kcal/mol in basic environments. Molecular dynamics (MD) simulations revealed parallel orientation for the ERY molecule's adsorption on AMD/ML53A with 80% rejection rate. In conclusion, our study highlighted the importance of modeling in developing practical solutions for removing antibiotics as PHCs from wastewater. The insights gained from our calculations can facilitate the design of more effective adsorption materials, ultimately leading to a more hygienic and sustainable ecosystem.
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Affiliation(s)
- Iman Salahshoori
- Department of Polymer Processing, Iran Polymer and Petrochemical Institute, Tehran, Iran; Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Majid Namayandeh Jorabchi
- Leibniz Institute for Catalysis, Albert-Einstein-Straße 29a, D-18059 Rostock, Germany; Department of Chemical Engineering, Quchan University of Technology, Quchan, Iran.
| | - Afsaneh Mazaheri
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Birjand, Birjand, Iran
| | | | - Mahdis Afshar
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mahdi Golriz
- Department of Polymer Processing, Iran Polymer and Petrochemical Institute, Tehran, Iran; Department of Energy Storage, Institute of Mechanics, Shiraz, Iran
| | - Marcos A L Nobre
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, 19060-900, Brazil
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Tetradentate square-planar acetylumbelliferone–nickel (II) complex formation: a DFT and TD-DFT study. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Hasan MS, Liton AK, Haque T, Ali MI, Akter S. An experimental and DFT computational study on Methyl 3-acetyl-2-oxo-2H-chromene-6-carboxylate. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2103468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Md. Sajid Hasan
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Abul Kashem Liton
- Department of Chemistry, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Tahmina Haque
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Idrish Ali
- Department of Chemistry, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Shathee Akter
- Department of Chemistry, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
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Wang XD, Tang M, Yi DJ, Shen QY, Ma JL. Cycling Na-O2 batteries via Li2O2 formation and Na deposition. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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An innovative rhein-matrine cocrystal: Synthesis, characterization, formation mechanism and pharmacokinetic study. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Mazurek AH, Szeleszczuk Ł, Gubica T. Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes. Int J Mol Sci 2021; 22:9422. [PMID: 34502331 PMCID: PMC8431145 DOI: 10.3390/ijms22179422] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022] Open
Abstract
Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host-guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.
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Affiliation(s)
- Anna Helena Mazurek
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Doctoral School, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
| | - Łukasz Szeleszczuk
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
| | - Tomasz Gubica
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
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Boulmokh Y, Belguidoum K, Meddour F, Amira-Guebailia H. Investigation of antioxidant activity of epigallocatechin gallate and epicatechin as compared to resveratrol and ascorbic acid: experimental and theoretical insights. Struct Chem 2021. [DOI: 10.1007/s11224-021-01763-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Zárate Hernández LA, Camacho-Mendoza RL, González-Montiel S, Cruz-Borbolla J. The chemical reactivity and QSPR of organic compounds applied to dye-sensitized solar cells using DFT. J Mol Graph Model 2021; 104:107852. [PMID: 33556645 DOI: 10.1016/j.jmgm.2021.107852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 01/23/2021] [Indexed: 11/19/2022]
Abstract
The structural and electronic properties were calculated for seventy organic compounds used as dye sensitizers in solar cells, applying the B3LYP exchange-correlation energy functional with the 6-311G∗∗ basis set. Moreover, the present study proposes two new quantitative structure-property relationship (QSPR) models that enable the prediction of the power conversion efficiency (PCE) and maximum absorption wavelength (λmax) of these systems, the two QSPR models were validated using the coefficient of determination (R2) of 0.62 for both models with the leave-one-out cross-validation correlation coefficient (Q2LOO) of 0.55 and 0.57, respectively. Furthermore, applicability domain analysis was conducted in order to identify the related compounds via the extrapolation of the model.
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Affiliation(s)
- Luis A Zárate Hernández
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma Del Estado de Hidalgo, Km. 14.5 Carretera Pachuca-Tulancingo, Ciudad Del Conocimiento, C.P. 42184, Mineral de la Reforma, Hidalgo, Mexico
| | - Rosa L Camacho-Mendoza
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma Del Estado de Hidalgo, Km. 14.5 Carretera Pachuca-Tulancingo, Ciudad Del Conocimiento, C.P. 42184, Mineral de la Reforma, Hidalgo, Mexico
| | - Simplicio González-Montiel
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma Del Estado de Hidalgo, Km. 14.5 Carretera Pachuca-Tulancingo, Ciudad Del Conocimiento, C.P. 42184, Mineral de la Reforma, Hidalgo, Mexico
| | - Julián Cruz-Borbolla
- Área Académica de Química, Centro de Investigaciones Químicas, Universidad Autónoma Del Estado de Hidalgo, Km. 14.5 Carretera Pachuca-Tulancingo, Ciudad Del Conocimiento, C.P. 42184, Mineral de la Reforma, Hidalgo, Mexico.
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Hansel K, Marietti R, Tramontana M, Bianchi L, Rigano L, Lionetti N, Romita P, Giuffrida R, Stingeni L. Sensitization/tolerance profile of betamethasone sodium phosphate in patients with contact allergy to budesonide. Dermatol Ther 2020; 33:e14155. [DOI: 10.1111/dth.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Katharina Hansel
- Dermatology Section, Department of Medicine University of Perugia Perugia Italy
| | - Rossella Marietti
- Dermatology Section, Department of Medicine University of Perugia Perugia Italy
| | - Marta Tramontana
- Dermatology Section, Department of Medicine University of Perugia Perugia Italy
| | - Leonardo Bianchi
- Dermatology Section, Department of Medicine University of Perugia Perugia Italy
| | - Luigi Rigano
- R&D Department ISPE (Institute of Skin and Product Evaluation) Milan Italy
| | - Nicola Lionetti
- R&D Department ISPE (Institute of Skin and Product Evaluation) Milan Italy
| | - Paolo Romita
- Department of Biomedical Science and Human Oncology, Dermatological Clinic University of Bari Bari Italy
| | - Roberta Giuffrida
- Department of Clinical and Experimental Medicine, Dermatology University of Messina Messina Italy
| | - Luca Stingeni
- Dermatology Section, Department of Medicine University of Perugia Perugia Italy
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Kumar P, Gruza B, Bojarowski SA, Dominiak PM. Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure-activity studies. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:398-408. [PMID: 30821272 DOI: 10.1107/s2053273319000482] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/09/2019] [Indexed: 12/31/2022]
Abstract
The transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of great importance in biology and chemistry. UBDB2018 can be applied either as a source of aspherical atomic scattering factors in a standard X-ray experiment (dmin ≃ 0.8 Å) instead of the independent atom model (IAM), and can therefore enhance the final crystal structure geometry and refinement parameters; or as a tool to reconstruct the molecular charge-density distribution and derive the electrostatic properties of chemical systems for which 3D structural data are available. The extended data bank has been extensively tested, with the focus being on the accuracy of the molecular electrostatic potential computed for important drug-like molecules, namely the HIV-1 protease inhibitors. The UBDB allows the reconstruction of the reference B3LYP/6-31G** potentials, with a root-mean-squared error of 0.015 e bohr-1 computed for entire potential grids which span values from ca 200 e bohr-1 to ca -0.1 e bohr-1 and encompass both the inside and outside regions of a molecule. UBDB2018 is shown to be applicable to enhancing the physical meaning of the molecular electrostatic potential descriptors used to construct predictive quantitative structure-activity relationship/quantitative structure-property relationship (QSAR/QSPR) models for drug discovery studies. In addition, it is suggested that electron structure factors computed from UBDB2018 may significantly improve the interpretation of electrostatic potential maps measured experimentally by means of electron diffraction or single-particle cryo-EM methods.
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Affiliation(s)
- Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sławomir Antoni Bojarowski
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
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Stingeni L, Rigano L, Lionetti N, Bianchi L, Tramontana M, Foti C, Romita P, Antelmi A, Bruze M, Isaksson M, Hansel K. Sensitivity to imidazoles/nitroimidazoles in subjects sensitized to methylchloroisothiazolinone/methylisothiazolinone: A simple coincidence? Contact Dermatitis 2018; 80:181-183. [DOI: 10.1111/cod.13158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Luca Stingeni
- Clinical, Allergological and Venereological Dermatology Section, Department of MedicineUniversity of Perugia Perugia Italy
| | - Luigi Rigano
- R&D DepartmentInstitute of Skin and Product Evaluation Milan Italy
| | - Nicola Lionetti
- Rigano Laboratories S.r.l., Milano, Italy, R&D DepartmentInstitute of Skin and Product Evaluation Milan Italy
| | - Leonardo Bianchi
- Clinical, Allergological and Venereological Dermatology Section, Department of MedicineUniversity of Perugia Perugia Italy
| | - Marta Tramontana
- Clinical, Allergological and Venereological Dermatology Section, Department of MedicineUniversity of Perugia Perugia Italy
| | - Caterina Foti
- Department of Biomedical Science and Human Oncology, Dermatological ClinicUniversity of Bari Bari Italy
| | - Paolo Romita
- Department of Biomedical Science and Human Oncology, Dermatological ClinicUniversity of Bari Bari Italy
| | - Annarita Antelmi
- Department of Occupational and Environmental DermatologySkåne University Hospital, Lund University Lund Sweden
| | - Magnus Bruze
- Department of Occupational and Environmental DermatologySkåne University Hospital, Lund University Lund Sweden
| | - Marléne Isaksson
- Department of Occupational and Environmental DermatologySkåne University Hospital, Lund University Lund Sweden
| | - Katharina Hansel
- Clinical, Allergological and Venereological Dermatology Section, Department of MedicineUniversity of Perugia Perugia Italy
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Liu W, Huang YL, Yin ZL, Ding ZY. Investigation on the decomposition process of sodium aluminate solution by spectroscopic and theoretical calculation. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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