Molecular dynamics simulation of novel diamino-functionalized hollow mesosilica spheres for adsorption of dyes from synthetic wastewater

Two heterocyclic azole compounds, 3-(2,3-dihydrobenzo[d]thiazol-2-yl)-4H-chromen-4-one ( SVS1 ) and 5-(1H-indol-3-yl)-4-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione ( SVS2 ) were obtained unexpectedly from 2-aminothiophenol and 4-oxo-4H-chromene-3-carbaldehyde (for SVS1 ), and ( E )-2-((1H-indol-3-yl)methylene)-N-methylhydrazine-1-carbothioamide in the presence of anhydrous FeCl 3 (for SVS2 ), respectively. The compounds were well characterized by analytical and spectroscopic tools. The molecular structures of both the compounds were determined by single crystal X-ray diffraction (X-RD) study. The results obtained from density functional theory (DFT) study revealed the molecular geometry and electron distribution of the compounds, which were correlated well with the three-dimensional structures obtained from the single crystal X-ray diffraction. DMol 3 was used to calculate quantum chemical parameters [chemical potential ( µ ), global hardness ( η ), global softness ( σ ), absolute electronegativity ( χ ) and electrophilicity index ( ω )] of SVS1 and SVS2 . Molecular docking study was performed to elucidate the binding ability of SVS1 and SVS2 with SARS-CoV-2 main protease and human angiotensin-converting enzyme-2 (ACE-2) molecular targets. Interestingly, the binding efficiency of the compounds with the molecular targets was comparable with that of remdesivir (SARS-CoV-2), chloroquine and hydroxychloroquine. SVS1 showed better docking energy than SVS2 . The molecular docking study was complemented by molecular dynamic simulation study of SARS-CoV-2 main protease- SVS1 complex, which further exemplified the binding ability of SVS1 with the target. In addition, SVS1, SVS2 and cisplatin were assessed for their cytotoxicity against a panel of three human cancer cells such as HepG-2 (hepatic carcinoma), T24 (bladder) and EA.hy926 (endothelial), as well as Vero (kidney epithelial cells extracted from an African green monkey) normal cells using MTT assay. The results showed that SVS2 has significant cytotoxicity against HepG-2 and EA.hy926 cells with the IC 50 values of 33.8 μM (IC 50 = 49.9 μM-cisplatin and 8.6 μM-doxorubicin) and 29.2 (IC 50 = 26.6 μM-cisplatin and 3.8 μM-doxorubicin), respectively.

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“…The hardness ( η ) of the compounds was calculated using Eq. 1 and values are given in Table 5 [40] .

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Section: Resultsmentioning

confidence: 99%

“…Material studio (DMol 3 ) software was used for optimization, and energy, HOMO (highest-occupied molecular orbital) and LUMO (lowest-unoccupied molecular orbital) calculations [40] of the compounds ( SVS1 and SVS2 ), and remdesivir, chloroquine and hydroxychloroquine drugs ( Fig. 1 ).…”

Section: Methodsmentioning

confidence: 99%

Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity

Haribabu

Garisetti

Malekshah

et al. 2022

Journal of Molecular Structure

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“…For designing different 3D structures of AmBisome, first, the conformers of the liposomes and Amp B ( Figure 2A ) were found in the National Center for Biotechnology Information (NCBI) PubChem compounds database ( www.pubchem.ncbi.nlm.nih.gov/ ) and were transferred in SDF plan. The Materials Studio software was employed for molecular quantum designs through the DMol3 segment ( Pelalak et al, 2021 ). Before the computational calculations, Hyperchem software was used to improve the geometry of Amp B and liposomes.…”

Section: Manuscript Formattingmentioning

confidence: 99%

Cytotoxicity of Amphotericin B and AmBisome: In Silico and In Vivo Evaluation Employing the Chick Embryo Model

et al. 2022

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Leishmaniasis has been identified as a significant disease in tropical and subtropical regions of the world, with Iran being one of the disease-endemic areas. Various treatments have been applied for this disease, and amphotericin B (Amp B) is the second line of treatment. Side effects of this drug have been reported in various organs. The present study investigated the effects of different types of Amp B on fetal organs using in silico and in vivo assays (chicken embryos). In vivo analysis was done by checking pathological changes, angiogenesis, and apoptosis alterations on eggs treated by Amp B and AmBisome. In silico approach was employed to predict the affinity of Amp B and AmBisome to the vascular endothelial growth factor A (VEGF-A), its receptor (KDR1), apoptotic-regulator proteins (Bcl-2-associated X protein (Bax), B-cell lymphoma (Bcl-2), and Caspase-8. The ADME-toxicity prediction reveals that AmBisome possesses a superior pharmacological effect to Amp B. The best result of all the dockings in the Molegro Virtual Docker (MVD) was obtained between Bax, Bcl-2, Caspase-8, KDR1, and VEGF-A targets. Due to the lower Egap (HOMO–LUMO) of AmBisome, the chemical reactivity of AmBisome was higher than that of Amp B. In vivo analysis showed that embryos that received Amp B exhibited less vascular density than AmBisome. Amp B alone significantly increased the expression of apoptosis and decreased angiogenesis genes compared to AmBisome. The histopathology analysis of the treated embryos showed a reduction in the blood vessel collapse and an increase in degenerative and apoptotic–necrotic changes in the embryonic tissues. Overall, the results suggest the potential benefits of AmBisome over Amp B, which might be a better treatment strategy to treat leishmaniasis during pregnancy.

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“…In order to propose and implement a high-performance model for prediction of adsorption process using hybrid materials with nanostructure, herein we demonstrate for the first time simulation of a novel Ni 50 Co 50 -LDH-COOH/UiO-66(Zr)-(COOH) 2 nanocomposite (LDH/MOF) in separation of Pb(II) and Cd(II) solutes from water considering various conditions by development of an artificial intelligence-based model 58 . Different adsorbents had been used as effective adsorbents for pollutant removal from aqueous media such as MOFs, natural materials, and mesoporous silica 59 – 62 . In the recent years, metal organic framework (MOF) adsorbents have attracted so many attentions for this application due to their fantastic properties 63 , 64 .…”

Section: Introductionmentioning

confidence: 99%

Neural-based modeling adsorption capacity of metal organic framework materials with application in wastewater treatment

Parsaei

Roudbari

Piri

et al. 2022

Sci Rep

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We developed a computational-based model for simulating adsorption capacity of a novel layered double hydroxide (LDH) and metal organic framework (MOF) nanocomposite in separation of ions including Pb(II) and Cd(II) from aqueous solutions. The simulated adsorbent was a composite of UiO-66-(Zr)-(COOH)2 MOF grown onto the surface of functionalized Ni50-Co50-LDH sheets. This novel adsorbent showed high surface area for adsorption capacity, and was chosen to develop the model for study of ions removal using this adsorbent. A number of measured data was collected and used in the simulations via the artificial intelligence technique. Artificial neural network (ANN) technique was used for simulation of the data in which ion type and initial concentration of the ions in the feed was selected as the input variables to the neural network. The neural network was trained using the input data for simulation of the adsorption capacity. Two hidden layers with activation functions in form of linear and non-linear were designed for the construction of artificial neural network. The model’s training and validation revealed high accuracy with statistical parameters of R2 equal to 0.99 for the fitting data. The trained ANN modeling showed that increasing the initial content of Pb(II) and Cd(II) ions led to a significant increment in the adsorption capacity (Qe) and Cd(II) had higher adsorption due to its strong interaction with the adsorbent surface. The neural model indicated superior predictive capability in simulation of the obtained data for removal of Pb(II) and Cd(II) from an aqueous solution.

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Molecular dynamics simulation of novel diamino-functionalized hollow mesosilica spheres for adsorption of dyes from synthetic wastewater

Cited by 78 publications

References 36 publications

Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity

Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity

Cytotoxicity of Amphotericin B and AmBisome: In Silico and In Vivo Evaluation Employing the Chick Embryo Model

Neural-based modeling adsorption capacity of metal organic framework materials with application in wastewater treatment

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