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Štekláč M, Breza M. DFT studies of camptothecins cytotoxicity IV — active and inactive forms of irinotecan. ACTA CHIMICA SLOVACA 2023. [DOI: 10.2478/acs-2023-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Abstract
Structures of irinotecan (CPT-11) in neutral lactone, neutral carboxyl, and anionic carboxylate forms in singlet ground states and of their complexes with Cu(II) in doublet ground states are optimized using B3LYP/6-311G* treatment. Metal ion affinities (MIA), Cu charges and Laplacians of Cu-ligand bond critical points of possible CPT active sites are evaluated. The formation of Cu(II) complexes with the anionic carboxylate ligand leads to the release of CO2 that can cause a decrease in the concentration of the active lactone form due to equilibria between all forms of the drug. MIA values and electron density transfer to Cu increase in the sequence lactone < neutral carboxyl < anionic carboxylate. Both neutral forms of irinotecan exhibit lower MIA values than those of camptothecin, unlike the anionic carboxylate form.
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Mittal A, Vashistha VK, Das DK. Recent advances in the antioxidant activity and mechanisms of chalcone derivatives: a computational review. Free Radic Res 2022; 56:378-397. [PMID: 36063087 DOI: 10.1080/10715762.2022.2120396] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this review, we have reported the antioxidant mechanisms and structure-antioxidant activity relationship of several chalcone derivatives, investigated in the recent past, based on the density functional theory (DFT) calculations, considering free radical scavenging and metal chelation ability. The antioxidant mechanisms include hydrogen atom transfer (HAT), sequential proton loss electron transfer (SPLET), single electron transfer followed by proton transfer (SET-PT), sequential proton loss hydrogen atom transfer (SPLHAT), sequential double proton loss electron transfer (SdPLET), sequential triple proton loss double electron transfer (StPLdET), sequential triple proton loss triple electron transfer (StPLtET), double HAT, double SPLET, double SET-PT, triple HAT, triple SET-PT, triple SPLET, proton-coupled electron transfer (PCET), single electron transfer (SET), radical adduct formation (RAF) and radical adduct formation followed by hydrogen atom abstraction (RAF-HAA). Furthermore, solvent effects have also been considered using different solvation models. The feasibility of scavenging different reactive oxygen and nitrogen species (ROS/RNS) has been discussed considering various factors such as the number and position of hydroxyl as well as methoxy groups present in the antioxidant molecule, stability of the species formed after scavenging reactive species, nature of substituent, steric effects, etc. This review opens new perspectives for designing new compounds with better antioxidant potential.
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Affiliation(s)
- Ankit Mittal
- Department of Chemistry, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Vinod Kumar Vashistha
- Department of Chemistry, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Dipak Kumar Das
- Department of Chemistry, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
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Kabanda MM, Bahadur I, Singh P. Antioxidant and anticancer properties of plant‐based bioactive flavonoids cardamonin and alpinetin: A theoretical insight from
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OOH antiradical and Cu (II) chelation mechanisms. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mwadham M. Kabanda
- Department of Chemistry, School of Natural and Mathematical Sciences, Faculty of Science, Engineering and Agriculture University of Venda Thohoyandou South Africa
| | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North‐West University South Africa
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi New Delhi India
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Sasa borealis Ethanol Extract Protects PC12 Neuronal Cells against Oxidative Stress. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The overproduction of reactive oxygen species (ROS) can cause oxidative stress to biomolecules such as nucleic acids, proteins, and lipids, leading to neurodegenerative disorders. Sasa borealis (SB) has antioxidant, anti-inflammatory, antidiabetic, and anti-obesity effects. We evaluated the neuroprotective activity of SB on hydrogen peroxide (H2O2)-induced oxidative stress. We investigated the antioxidant and neuroprotective effects of SB water extract (SBW) and SB ethanol extract (SBE) by measuring the radical scavenging activities and intracellular ROS production. SBE, which had a high level of isoorientin, had higher antioxidative activities than SBW in 2,2′-azino-bis-(3-ethylbenzothiazolin-6-sulfonic acid) diammonium salt (ABTS+) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays. It also reduced ROS generation in pheochromocytoma 12 (PC12) cells more significantly than SBW. It increased the translation of heme oxygenase-1 (HO-1), superoxide dismutase 2 (SOD2), catalase (CAT), and glutathione peroxidase (GPx) with a corresponding increase in the translation of NF-E2-related factor-2 (Nrf-2). In conclusion, SBE with high levels of phenolic compounds such as isoorientin shows promise for preventing neurodegenerative diseases.
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Štekláč M, Breza M. DFT studies of camptothecins cytotoxicity II. Protonated lactone forms of camptothecin. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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6
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DFT studies of camptothecins cytotoxicity III: camptothecin, irinotecan and SN-38. ACTA CHIMICA SLOVACA 2022. [DOI: 10.2478/acs-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Geometries of camptothecin, irinotecan, SN-38, and of their hypothetical Cu(II) complexes were optimized at the B3LYP/6-311G* level of theory. Their electron structure, evaluated in terms of Mulliken population analysis and Quantum Theory of Atoms-in-Molecule, was subsequently related to in vitro cytotoxicity. Electron density transfer from the relevant active sites to Cu decreases in the sequence irinotecan > SN-38 > camptothecin. The absolute values of their metal-ligand interaction energies exhibit the same trend. Discrepancy with the least relative in vitro cytotoxicity of irinotecan can be explained by differences in its pharmacokinetics.
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Štekláč M, Breza M. DFT Studies of Substituted Phenols Cytotoxicity I.
Para
‐substituted Phenols. ChemistrySelect 2021. [DOI: 10.1002/slct.202101568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marek Štekláč
- Department of Physical Chemistry Faculty of Chemical and Food Technology Slovak Technical University, SK- 81237 Bratislava Slovakia
| | - Martin Breza
- Department of Physical Chemistry Faculty of Chemical and Food Technology Slovak Technical University, SK- 81237 Bratislava Slovakia
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Madala NE, Kabanda MM. LC-MS based validation and DFT investigation on the antioxidant properties of clovamide: •OH and •OOH scavenging and Cu(II) chelation mechanisms. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Khoirunisa V, Rusydi F, Boli LSP, Saputro AG, Rachmawati H, Nakanishi H, Kasai H, Dipojono HK. Computational Investigation on the ∙OOH Scavenging Sites of Gnetin C. FOOD BIOPHYS 2021. [DOI: 10.1007/s11483-021-09666-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Quantum-chemical studies of rutile nanoparticles toxicity II. Comparison of B3LYP and PM6 data. ACTA CHIMICA SLOVACA 2021. [DOI: 10.2478/acs-2021-0006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The relation between copper atomic charges and metal-ligand interaction energies obtained by PM6 and DFT-B3LYP methods for cytotoxicity prediction of model rutile nanoparticles [Ti40O124H81]7–, [Ti7O28H26]2–, [Ti2O10H10]2–, [Ti7O30H30]2– and their Cu(II) complexes is investigated. Except for Mulliken charges, very good statistical parameters were obtained for the linear relation between the results obtained by both methods if standard accuracy of quantum-chemical calculations is achieved.
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Comparative DFT study of the effectiveness of p-phenylenediamine antioxidants through their coordination ability towards the late 1st row transition metals. Polym Degrad Stab 2021. [DOI: 10.1016/j.polymdegradstab.2020.109438] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Kabanda MM, Gbashi S, Madala NE. Proportional coexistence of okanin chalcone glycoside and okanin flavanone glycoside in Bidens pilosa leaves and theoretical investigation on the antioxidant properties of their aglycones. Free Radic Res 2020; 55:53-70. [PMID: 33267705 DOI: 10.1080/10715762.2020.1859107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bidens pilosa plant has been shown to produce okanin flavanone glycoside and its chalcone derivative. In most other plants, due to chalcone isomerase enzyme, the flavanone tends to exist in higher proportions than their chalcone precursors. Herein we have utilized liquid chromatography-mass spectrometry approach and shown that within the leaves of Bidens pilosa plant the two okanin glycosides exist in unusual equal proportional distribution, which indicates that Bidens pilosa plant is an alternative rich source of these highly sought-after antioxidant molecules. The aglycone okanin chalcone (ONC) and okanin flavanone (ONF) have experimentally been shown to exhibit antioxidant activity. However, experimental findings have not conclusively determined which of the two compounds is a more potent antiradical than the other. Herein, the density functional theory (DFT) method is utilized to establish, from structural and thermodynamic energetic considerations, the preferred antioxidant molecule between the two aglycone okanins. A theoretical study on the antioxidant properties of ONC and ONF has been performed by considering their radical scavenging and metal cation (Mn+, where M = Cu(II) or Fe (III)) chelation ability. The study has been performed using B3LYP/6-31 + G(d,p) method. In the case of the metal chelation mechanism, the LANL2DZ pseudo-potential was selected to describe the selected Mn+ cations. The results of the study suggest that ONC is a better radical scavenger than ONF because of the extended electron delocalization on its neutral radical, which is due to the presence of conjugation within the ONC neutral radical after hydrogen atom abstraction. In the metal chelation mechanism, it is noted that the binding energies depend on the media, the nature of the ligand and the cation and the cation coordination site on the ligand. The charge and the spin density on Mn+ decrease on coordination to the ligand. The ability of the ligands to reduce Mn+ cations, coupled with the strong Mn+ binding properties, has significant implication on the antioxidant ability of both okanins. However, since ONC⋅⋅⋅M+n interaction results in higher binding energy than ONF⋅⋅⋅M+n interaction, the implication is that ONC is a preferred free metal ion chelator than ONF.
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Affiliation(s)
- Mwadham M Kabanda
- Department of Chemistry, University of Venda, Thohoyandou, South Africa
| | - Sefater Gbashi
- Department of Biotechnology and Food Technology, University of Johannesburg, Auckland Park, South Africa
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Otukile KP, Kabanda MM. A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.
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Affiliation(s)
- Kgalaletso P. Otukile
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
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Serobatse KR, Kabanda MM. An appraisal of the hydrogen atom transfer mechanism for the reaction between thiourea derivatives and OH radical: A case-study of dimethylthiourea and diethylthiourea. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Serobatse KRN, Kabanda MM. A theoretical study on the antioxidant properties of methoxy-substituted chalcone derivatives: A case study of kanakugiol and pedicellin through their Fe (II and III) coordination ability. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500486] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical study on the antioxidant properties of two chalcone derivatives, kanakugiol and pedicellin, is performed by considering their Fe[Formula: see text] and Fe[Formula: see text] coordination ability. The objective of the study is to elucidate the factors influencing the stability of the isolated conformers, the nature of the complexes, metal[Formula: see text]ligand stability, metal ion affinities (MIA) and electronic properties of the cations before and after coordination to the ligand. The study is performed using the B3LYP/6–311[Formula: see text]G(2d,p)//B3LYP/6–31[Formula: see text]G(d,p) method. The LANL2DZ pseudopotential is selected to describe the Fe[Formula: see text] ions. Time-dependent density functional theory (TDDFT) method is used to assess the electronic UV–Vis spectra of the isolated chalcones and their complexes with Fe[Formula: see text] ions. The results suggest that the preferred complexes are those in which the Fe ion is coordinated at the hydroxyl-methoxy and hydroxyl-keto sites for kanakugiol and methoxy-keto site for pedicellin. Both kanakugiol and pedicellin have potential to chelate iron ions as demonstrated by their high MIA values in vacuo and in water solution. However, the ability of pedicellin to chelate iron is slightly lower than that of kanakugiol, indicating that the presence of the hydroxyl group has an effect of enhancing the metal binding abilities of the chalcone derivatives. In all the complexes obtained in vacuo, kanakugiol and pedicellin exhibit the ability to reduce the Fe[Formula: see text] ion. In water solution (which mimics the environment in biological systems or studies performed in vivo), Fe[Formula: see text] is reduced to Fe[Formula: see text] upon coordination to the ligand while the oxidation number of Fe[Formula: see text] upon coordination to the ligand remains virtually unchanged.
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Affiliation(s)
- Kemoabetswe R. N. Serobatse
- Faculty of Agriculture, Science and Technology, School of Mathematical and Physical Science, Department of Chemistry, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Faculty of Agriculture, Science and Technology, School of Mathematical and Physical Science, Department of Chemistry, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
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Makola MM, Madala NE, Dubery IA, Steenkamp PA, Kabanda MM. Influence of the geometric isomers on the radical scavenging properties of 3,5-dicaffeoylquinic acid: A DFT study in vacuo and in solution. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
3,5-Dicaffeoylquinic acid (diCQA) is a part of the chlorogenic acid group of compounds, largely isolated from food sources and possessing potent antioxidant activity. Only the trans–trans isomer exists in nature, however, abiotic stresses, such as UV-radiation, give rise to cis isomers. There have been no reports on the antioxidant activity of the cis isomers. The current study, performed using the B3LYP/6-311[Formula: see text]G(d,p) method, is aimed at investigating and comparing the antioxidant properties of the geometrical isomers of 3,5-diCQA. The study is conducted by checking the molecules’ ability for two main radical scavenging mechanisms, hydrogen atom transfer (HAT) and electron transfer (ET). A separate DPPH assay experimental study performed in this study shows that all the geometrical isomers are potent radical scavengers. The lowest O[Formula: see text]H bond dissociation enthalpy value (70.599 kcal/mol) corresponds to the trans–trans isomer and is comparable to that of gallic acid, a commercially available antioxidant. The lowest ionization potential value corresponds to the cis–cis isomer (149.54[Formula: see text]kcal/mol), indicating that it is best antioxidant, in terms of ET mechanism.
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Affiliation(s)
- Mpho M. Makola
- Department of Biochemistry, University of Johannesburg P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry, University of Johannesburg P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Paul A. Steenkamp
- Council for Scientific and Industrial Research (CSIR), Biosciences, Natural Products and Agroprocessing Group, Pretoria 0001, South Africa
| | - Mwadham. M. Kabanda
- Department of Chemistry, Faculty of Agriculture, Science and Technology, School of Mathematical and Physical Science, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
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Synthesis, crystal structure, thermal and theoretical studies of bis(N-ethyl-N-phenyldithiocarbamato) Ni(II) and (N-ethyl-N-phenyldithiocarbamato) (isothiocyanato) (triphenylphosphine) Ni(II). J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1111-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zuriaga-Monroy C, Oviedo-Roa R, Montiel-Sánchez LE, Vega-Paz A, Marín-Cruz J, Martínez-Magadán JM. Theoretical Study of the Aliphatic-Chain Length’s Electronic Effect on the Corrosion Inhibition Activity of Methylimidazole-Based Ionic Liquids. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b03884] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carolina Zuriaga-Monroy
- Instituto Mexicano del Petróleo,
Lázaro Cárdenas Norte 152, San Bartolo Atepehuacán 07730, México, D.F. México
| | - Raúl Oviedo-Roa
- Instituto Mexicano del Petróleo,
Lázaro Cárdenas Norte 152, San Bartolo Atepehuacán 07730, México, D.F. México
| | - Luisa E. Montiel-Sánchez
- Instituto Mexicano del Petróleo,
Lázaro Cárdenas Norte 152, San Bartolo Atepehuacán 07730, México, D.F. México
| | - Araceli Vega-Paz
- Instituto Mexicano del Petróleo,
Lázaro Cárdenas Norte 152, San Bartolo Atepehuacán 07730, México, D.F. México
| | - Jesús Marín-Cruz
- Instituto Mexicano del Petróleo,
Lázaro Cárdenas Norte 152, San Bartolo Atepehuacán 07730, México, D.F. México
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Antioxidant and antimalarial properties of butein and homobutein based on their ability to chelate iron (II and III) cations: a DFT study in vacuo and in solution. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2520-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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A theoretical study of the antioxidant properties of phenolic acid amides investigated through the radical-scavenging and metal chelation mechanisms. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2484-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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