Molecular dynamic simulations and quantum chemical calculations of adsorption process using amino-functionalized silica

Molecular simulation-based insights into dye pollutant adsorption: A perspective review

Growing concerns about environmental pollution have highlighted the need for efficient and sustainable methods to remove dye contamination from various ecosystems. In this context, computational methods such as molecular dynamics (MD), Monte Carlo (MC) simulations, quantum mechanics (QM) calculations, and machine learning (ML) methods are powerful tools used to study and predict the adsorption processes of dyes on various adsorbents. These methods provide detailed insights into the molecular interactions and mechanisms involved, which can be crucial for designing efficient adsorption systems. MD simulations, detailing molecular arrangements, predict dyes' adsorption behaviour and interaction energies with adsorbents. They simulate the entire adsorption process, including surface diffusion, solvent layer penetration, and physisorption. QM calculations, especially density functional theory (DFT), determine molecular structures and reactivity descriptors, aiding in understanding adsorption mechanisms. They identify stable adsorption configurations and interactions like hydrogen bonding and electrostatic forces. MC simulations predict equilibrium properties and adsorption energies by sampling molecular configurations. ML methods have proven highly effective in predicting and optimizing dye adsorption processes. These models offer significant advantages over traditional methods, including higher accuracy and the ability to handle complex datasets. These methods optimize adsorption conditions, clarify adsorbent functionalization roles, and predict dye removal efficiency under various conditions. This research explores MD, MC, QM, and ML approaches to connect molecular interactions with macroscopic adsorption phenomena. Probing these techniques provides insights into the dynamics and energetics of dye pollutants on adsorption surfaces. The findings will aid in developing and optimizing new materials for dye removal. This review has significant implications for environmental remediation, offering a comprehensive understanding of adsorption at various scales. Merging microscopic data with macroscopic observations enhances knowledge of dye pollutant adsorption, laying the groundwork for efficient, sustainable removal technologies. Addressing the growing challenges of ecosystem protection, this study contributes to a cleaner, more sustainable future.

Boosting ciprofloxacin and indigo carmine dye photodegradation using S-scheme plate-like BiOI@sulfated TiO2 heterojunctions: An understanding of the performance, the degradation route, and DFT computation

Sustainable BiOI/sulfated TiO2 nanocomposites were created for the present study utilizing the environmentally friendly dispersion-ultrasonication technique. Then, their ability to degrade the medication ciprofloxacin (CIP) and indigo carmine coloring (IC) in aquatic water was evaluated. The optimized catalyst 10%BiOI/ST, denoted as 10BOST together with 5BOST, is subjected to thorough characterization together with that of sulfate-free TiO2 (10BOT) to assess their physiochemical, morphological, textural, structural, and elemental composition properties. It is noteworthy that the 10BOST composite achieves remarkable degradation and performs exceptionally well in photocatalytic IC and CIP degradation. In 35 min, it degrades IC to 100%, with a rate constant of 0.066 min-1, which is superior to that of 10BOT (0.054 min-1) in the incidence of visible light and without an oxidizing agent. In CIP, 10BOST yields 85.6% degradation with a rate constant of 0.027 min-1 preceding 0.024 min-1 for 10BOT when potassium persulfate oxidizing agent is present. This exceptional performance is ascribed to the composite's diminished particle diameter, largest pore radius, hydrophilicity, improved light absorption, and the developed heterojunction between ST and BiOI, as demonstrated by XPS, TEM, XRD, EDX and IR data. The effect of sulfation concentration, pH, Ti3+/Ti4+ ratio, and pollutant concentration were studied together with the active species determinations, which revealed that active radicals like SO4•-, •OH, and h+ were well participated in the pollutant's decomposition. Testing for toxicity shows that during CIP breakdown, innocuous hazardous intermediates evolve with a notable 70% mineralization rate in their TOC. Furthermore, 10BOST showed strong stability and reusability. Using DFT simulations, profound insights into the principles underlying the adsorption sites of pollutants, their chemical reactivity, and the arrangement of their electrical charges, and how these factors affect the reaction mechanism on BOST photocatalysts.

Exploring the potential of beta-cyclodextrin-based MIL-101(Cr) for pharmaceutical removal from wastewater: A combined density functional theory and molecular simulations study

Pharmaceutical contaminants pose significant risks to ecosystems and human health, necessitating effective removal strategies. This research focuses on developing advanced adsorbents for removing pharmaceutical pollutants from the environment. Metal-organic frameworks (MOFs), specifically MIL-101(Cr) functionalized with biodegradable beta-cyclodextrin (β-CDex), were investigated as potential nanocomposite adsorbents for the removal of ketorolac (KTRK), naproxen (NPXN), and tramadol (TRML). The study employed molecular simulations and density functional theory (DFT) calculations to explore the interactions between the pollutants and adsorbents. Analyses of DFT results, including electrostatic potential, ionization energy, density of states, and molecular orbital analysis, provided insights into the reactivity of pollutants and adsorbents. Additionally, the structural properties of the adsorbents, such as fractional free volume, radius of gyration, and system energies, were thoroughly examined. Molecular dynamics (MD) and Monte Carlo (MC) simulations were used to evaluate the adsorption capacities of MIL-101(Cr) for the target pharmaceutical pollutants. The results demonstrated the superior adsorption performance of the nanocomposite adsorbent, particularly for KTRK, with an adsorption energy of -1934 kcal/mol, compared to the pristine MIL-101(Cr), which had an adsorption energy of -1916 kcal/mol. This enhanced adsorption is attributed to the optimal molecular fit, guest-host solid interactions, and the selective encapsulation capabilities of β-CDex. This research highlights the potential of MOF-based nanocomposites as effective and sustainable solutions for pharmaceutical pollution. By advancing the understanding of molecular interactions through simulations, this study contributes to developing innovative adsorbents for wastewater treatment and the protection of water resources.

Tackling antibiotic contaminations in wastewater with novel Modified-MOF nanostructures: A study of molecular simulations and DFT calculations

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.

Application of Mesoporous Silicas for Adsorption of Organic and Inorganic Pollutants from Rainwater

Precipitation is an important factor that influences the quality of surface water in many regions of the world. The pollution of stormwater runoff from roads and parking lots is an understudied area in water quality research. Therefore, a comprehensive analysis of the physicochemical properties of rainwater flowing from parking lots was carried out, considering heavy metals and organic micropollutants. High concentrations of zinc were observed in rainwater, in addition to alkanes, e.g., tetradecane, hexadecane, octadecane, 2,6,10-trimethyldodecane, 2-methyldodecane; phenolic derivatives, such as 2,6-dimethoxyphenol and 2,4-di-tertbutylphenol; and compounds such as benzothiazole. To remove the contaminants present in rainwater, adsorption using silica carriers of the MCF (Mesostructured Cellular Foams) type was performed. Three groups of modified carriers were prepared, i.e., (1) SH (thiol), (2) NH2 (amino), and (3) NH2/SH (amine and thiol functional groups). The research problem, which is addressed in the presented article, is concerned with the silica carrier influence of the functional group on the adsorption efficiency of micropollutants. The study included an evaluation of the effects of adsorption dose and time on the efficiency of the contaminant removal process, as well as an analysis of adsorption isotherms and reaction kinetics. The colour adsorption from rainwater was 94-95% for MCF-NH2 and MCF-NH2/SH. Zinc adsorbance was at a level of 90% for MCF-NH2, and for MCF-NH2/SH, 52%. Studies have shown the high efficacy (100%) of MCF-NH2 in removing organic micropollutants, especially phenolic compounds and benzothiazole. On the other hand, octadecane was the least susceptible to adsorption in each case. It was found that the highest efficiency of removal of organic micropollutants and zinc ions was obtained through the use of functionalized silica NH2.

Facile engineering of mesoporous silica for the effective removal of anionic dyes from wastewater: Insights from DFT and experimental studies

The discharge of dye effluents from the textile industries has become a major environmental issue due to its potential to impart serious harm to human health and aquatic life. Mesoporous silica due to its high chemical stability, large surface area, tunable morphologies, large pore volume and pore size and cost-effectiveness is commonly used to remove such dyes before recycling of the wastewater for agricultural, domestic, and industrial applications. However, the low colloidal stability, the fast aggregation of the silica particles and the slow etching of the silica surface often results in the fast deactivation of the adsorbents and limits their long-term applications. In this study, we report the functionalization of mesoporous silica (SBA-15) with ZnO nanoparticles for the effective removal of anionic dyes. The Zn-silica exhibited highly positive surface with a dipole moment of 172 Debye and high charge transfer efficacy with an energy bandgap (ΔE) of 3.35 eV as revealed by quantum chemical DFT simulations. It achieved excellent removal of Alizarin red dye reaching a removal efficiency of 99.99 % and an adsorption capacity of 50 mg/g. In the presence of heavy metal ions commonly present in wastewater (Cd2+, Co2+, Zn2+, Ni2+, Cu2+ and Hg2+), the Zn-silica maintain excellent stability, high selectivity, and reusability within 5 cycles without a significant decline in efficiency. This study thus presents an effective way of wastewater purification on cost-effective adsorbents for meeting the water scarcity demands.

Amino-functionalization of lignocellulosic biopolymer to be used as a green and sustainable adsorbent for anionic contaminant removal

In this work, natural biopolymer stemming from lignocellulosic peanut hull biomass was used as a green and low-cost adsorbent to eliminate anionic Congo red (CR) and Cr(VI) ions from aqueous sample. In order to enhance the removal performance, the lignocellulosic biopolymer was subjected to amino-modification by the graft copolymerization of (3-acrylamidopropyl) trimethylammonium chloride and N, N'-methylenebisacrylamide. The property of the prepared amino-functionalized biopolymer (AFB) was examined through FTIR, TG, SEM, particle size analysis, zeta potential determination and XPS. The adsorption efficacy of AFB for CR and Cr(VI) was tested at different pH, contact time and initial concentration. The kinetic, isotherm and thermodynamics investigations revealed that the uptakes of CR and Cr(VI) were the combination processes of chemical and physical interactions, and both endothermic in nature. The AFB exhibited good reusability without significant loss in adsorption capacity after five consecutive cycles. Mechanistic analysis indicated that the quaternary ammonium groups in AFB contributed a lot to the binding of anionic compounds through electrostatic attraction. In addition, n-π and hydrogen bonding while reduction and coordination were also responsible for the removal of CR and Cr(VI), respectively. The present study provides a favorable strategy for the removal of anionic contaminates in water by using green and sustainable lignocellulosic wastes.

Fabrication and examination of polyorganophosphazene/polycaprolactone-based scaffold with degradation, in vitro and in vivo behaviors suitable for tissue engineering applications

The present study aimed to synthesis a proper scaffold consisting of hydroxylated polyphosphazene and polycaprolactone (PCL), focusing on its potential use in tissue engineering applications. The first grafting of PCL to poly(propylene glycol)phosphazene (PPGP) was performed via ROP of ε-caprolactone, whereas PPGP act as a multisite macroinitiator. The prepared poly(propylene glycol phosphazene)-graft-polycaprolactone (PPGP-g-PCL) were evaluated by essential tests, including NMR, FTIR, FESEM-EDS, TGA, DSC and contact angle measurement. The quantum calculations were performed to investigate molecular geometry and its energy, and HOMO and LUMO of PPGP-g-PCL in Materials Studio2017. MD simulations were applied to describe the interaction of the polymer on phospholipid membrane (POPC128b) in Material Studio2017. The C2C12 and L929 cells were used to probe the cell-surface interactions on synthetic polymers surfaces. Cells adhesion and proliferation onto scaffolds were evaluated using FESEM and MTT assay. In vitro analysis indicated enhanced cell adhesion, high proliferation rate, and excellent viability on scaffolds for both cell types. The polymer was further tested via intraperitoneal implantation in mice that showed no evidence of adverse inflammation and necrosis at the site of the scaffold implantation; in return, osteogenesis, new-formed bone and in vivo degradation of the scaffold were observed. Herein, in vitro and in vivo assessments confirm PPGP-g-PCL, as an appropriate scaffold for tissue engineering applications.

Theoretical and experimental study of the photodegradation of methyl orange in the presence of different morphologies of Au-ZnO using Monte Carlo dynamic simulation

Herein, a simple approach was formed based on synthesizing different morphologies of ZnO and Au-ZnO as photocatalyst. In this study, ZnO and Au-ZnO were synthesized via a co-precipitation method and fully characterized via scanning electron microscopy (SEM), X-ray diffraction (XRD), and energy-dispersive X-ray spectroscopy (EDX). Three different ratios of Zn2+:OH- (1:2, 1:3, and 1:5) controlled the morphology of samples, which were made into spindle, star, and flower structures, respectively. Then, the photocatalytic activity was studied and compared. Their comparison showed that the flower morphology for ZnO and Au-ZnO was more effective in photocatalytic degradation and decolorization of methyl orange dye. Also, quantum and Monte Carlo (MC) calculations were carried out to investigate the adsorption of methyl orange (MO) molecules on ZnO(111) surface in the presence of Au or without Au in aqueous conditions by Monte Carlo adsorption locator simulations in the Materials Studio 2017 software. Au created a tendency to form a relatively strong interaction of MO with the ZnO(111) surface. The adsorption of MO on Au-ZnO(111) in the presence of Au was more significant than that of MO on ZnO(111), suggesting Au could significantly improve the reactivity of the methyl orange toward the ZnO(111).

Modeling the Liquid-Phase Adsorption of Cephalexin onto Coated Iron Nanoparticles Using Response Surface and Molecular Modeling

In order to assess the interactions between process factors, the experiments involving the liquid-phase adsorption of cephalexin (CEX) onto silicon-coated iron nanoparticles (Fe3O4@SIO2) were designed using the Box-Behnken Design-Response surface methodology (BBD-RSM). Optimal circumstances were used to investigate the synergistic influence on the process’s efficiency. In addition, the data was used to test and fit an artificial neural network (ANN) model. Molecular-level DFT calculations on the CEX molecule were carried out. The PW6B95D3/Def2-TZVP level of theory was used to build DFT-based descriptors for the CEX molecule. At 25°C, pH 5.83, 37.67 min, a dosage of 0.8 g Fe3O4@SIO2 and 118.01 mg/L CEX, the removal efficiency achieved a maximum of 99.01 percent. For example, we found that OH --- O, NH --- O, CH --- O hydrogen bonds, NH --- π, OH --- π, CH --- π interactions as well as dipole-dipole interactions between CEX and the nanoparticles could all be used to connect the CEX and the nanoparticles. There is a strong correlation between the output and target values acquired by BBD-RSM and ANN fits. Fe3O4@SIO2 proved to be an excellent tool for eliminating CEX.

Discovery of Natural Rosin Derivatives Containing Oxime Ester Moieties as Potential Antifungal Agents to Control Tomato Gray Mold Caused by Botrytis cinerea

Inspired by the application of natural products against pathogenic fungi, two series of dehydroabietyl oxime ester derivatives were synthesized using rosin as a raw material. Based on the evaluation and screening of in vitro antifungal activities against Botrytis cinerea (B. cinerea), Sclerotinia sclerotiorum, Valsa mali, Rhizoctonia solani, Fusarium oxysporum, and Alternaria alternata, compound 4f exhibited the best antifungal activity against B. cinerea, and its EC₅₀ was 0.798 mg/L, which was lower than that of the positive control trifloxystrobin (1.112 mg/L). The in vivo antifungal activity results showed that 4f had satisfactory protective and curative effects on tomato. Physiological and biochemical studies showed that the action mechanism of compound 4f against B. cinerea is to change the morphology and the ultrastructure of the mycelium, increase the permeability of the cell membrane, and cause nucleus and mitochondrial dysfunction, thus leading to apoptosis. In addition, qualitative and quantitative structure-activity relationship studies showed that the inductive and conjugative interactions between compound 4f and the target receptor form an electron transfer process, thereby achieving an antifungal effect. These results indicated that compound 4f, which was derived from the natural product rosin, is a novel potential fungicidal candidate against B. cinerea.

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

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.

Epichlorohydrin and tripolyphosphate-crosslinked chitosan-kaolin composite for Auramine O dye removal from aqueous solutions: Experimental study and DFT calculations

Chitosan (Ch, a natural polymer) and kaolin (K, a natural mineral) composite (Ch-K) was produced with the help of two crosslinkers, epichlorohydrin and tripolyphosphate, and then moulded into uniform beads in tripolyphosphate solution. The synthesis was proved by the analyses involving FT-IR and SEM-EDX. The beads were then used as the natural adsorbent for removal of the auramine O (AO), a frequently-used industrial dye, in aqueous solutions. Adsorbent performance of the Ch-K composite for AO dye molecules was optimized: 500 mg L^-1 at pH 7.5 at 25 °C. The Langmuir model found 0.118 mol kg^-1 for the maximum adsorption capacity of the Ch-K and the D-R isotherm model showed that the nature of the adsorption process was physical. Kinetics of the adsorption could be explained by using both IPD (intraparticle diffusion) and PSO (pseudo second order) models. Thermodynamic parameters demonstrated that the behaviour of the adsorption was an endothermic and spontaneous. The activity of the composite adsorbent was recovered (88%) after the five sequential adsorption/desorption cycles. Supported by experimental findings, the results obtained from in silico modeling at M06-2X/6-31+G (d,p) level helped hypothesise a mechanism for the formation of the Ch-K composite, and shed some light onto the adsorption behaviour of AO dye by assuming several favourable intermolecular interactions.

How β-cyclodextrin- loaded mesoporous SiO2 nanospheres ensure efficient adsorption of rifampicin

In this study, β-CD@mesoporous SiO₂ nanospheres (β-CD@mSi) were prepared by loading β-cyclodextrin (β-CD) onto mesoporous silica nanospheres through an in situ synthesis. This not only solved the defect of β-CD being easily soluble in water, but also changed the physical structure of the mesoporous silica nanospheres. FTIR and XPS results showed that β-CD was successfully loaded onto mesoporous silica nanospheres (mSi), while enhancing the adsorption effect. β-CD@mSi with a monomer diameter of about 150 nm were prepared. At a temperature of 298k, the removal efficiency of a 100 mg/L solution of rifampicin can reach 90% in 4 h and the adsorption capacity was 275.42 mg g^-1 at high concentration. Through the calculation and analysis of adsorption kinetics, adsorption isotherms and adsorption thermodynamics based on the experimental data, the reaction is a spontaneous endothermic reaction dominated by chemical adsorption. The electron transfer pathway, structure-activity relationship and energy between β-CD@mSi and rifampicin were investigated by quantum chemical calculations. The accuracy of the characterization test results to judge the adsorption mechanism was verified, to show the process of rifampicin removal by β-CD@mSi more clearly and convincingly. The simulation results show that π-π interaction plays a major interaction in the reaction process, followed by intermolecular hydrogen bonding and electrostatic interactions.

Molecular separation of ions from aqueous solutions using modified nanocomposites

Herein, two novel porous polymer matrix nanocomposites were synthesized and used as adsorbents for heavy metal uptake. Methacrylate-modified large mesoporous silica FDU-12 was incorporated in poly(methyl methacrylate) matrix through an in-situ polymerization approach. For another, amine-modified FDU-12 was composited with Nylon 6,6 via a facile solution blending protocol. Various characterization techniques including small-angle X-ray scattering, FTIR spectroscopy, field emission-scanning electron microscopy, transmission electron microscopy, porosimetry, and thermogravimetric analysis have been applied to investigate the physical and chemical properties of the prepared materials. The adsorption of Pb(II) onto the synthesized nanocomposites was studied in a batch system. After study the effect of solution pH, adsorbent amount, contact time, and initial concentration of metal ion on the adsorption process, kinetic studies were also conducted. For both adsorbents, the Langmuir and pseudo-second-order models were found to be the best fit to predict isotherm and kinetics of adsorption. Based on the Langmuir model, maximum adsorption capacities of 105.3 and 109.9 mg g-1 were obtained for methacrylate-modified FDU-12/poly(methyl methacrylate) and amine-modified FDU-12/Nylon 6,6, respectively.