Adsorption of acridine orange and methylene blue synthetic dyes and anthracene on single wall carbon nanotubes: A first principle approach

Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis

CONTEXT

Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C-O type bond, and exhibiting a hydrophilic surface characteristic (36.2°).

METHODS

Computational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.

Ab initio study of water anchored in graphene pristine and vacancy-type defects

CONTEXT

In this paper, we have addressed two issues that are relevant to the interaction of water in pristine and vacant graphene through first-principles calculations based on the Density Functional Theory (DFT). The results showed that for the interaction of pristine graphene with water, the DOWN configuration (with the hydrogen atoms facing downwards) was the most stable, presenting binding energies in the order of -13.62 kJ/mol at a distance of 2.375 Å in the TOP position. We also evaluated the interaction of water with two vacancy models, removing one carbon atom (Vac-1C) and four atoms (Vac-4C). In the Vac-1C system, the most favourable system was the DOWN configuration, with binding energies ranging from -20.60 kJ/mol to -18.41 kJ/mol in the TOP and UP positions, respectively. A different behaviour was observed for the interaction of water with Vac-4C; regardless of the configuration of the water, it is always more favourable for the interaction to occur through the vacancy centre, with binding energies ​​between -13.28 kJ/mol and -20.49 kJ/mol. Thus, the results presented open perspectives for the technological development of nanomembranes as well as providing a better understanding of the wettability effects of graphene sheets, whether pristine or with defects.

METHOD

We evaluated the interaction of pristine and vacant graphene with the water molecule, through calculations based on Density Functional Theory (DFT); implemented by the SIESTA program. The electronic, energetic, and structural properties were analyzed by solving self-consistent Kohn-Sham equations. In all calculations, a double ζ plus a polarized function (DZP) was used for the numerical baise set. Local Density Approximation (LDA) with the Perdew and Zunger (PZ) parameterisation along with a basis set superposition error (BSSE) correction were used to describe the exchange and correlation potential (Vxc). The water and isolated graphene structures were relaxed until the residual forces were less than 0.05 eV/Å^-1 in all atomic coordinates.

Oxygenated Hydrocarbons from Catalytic Hydrogenation of Carbon Dioxide

Once fundamental difficulties such as active sites and selectivity are fully resolved, metal-free catalysts such as 3D graphene or carbon nanotubes (CNT) are very cost-effective substitutes for the expensive noble metals used for catalyzing CO2. A viable method for converting environmental wastes into useful energy storage or industrial wealth, and one which also addresses the environmental and energy problems brought on by emissions of CO2, is CO2 hydrogenation into hydrocarbon compounds. The creation of catalytic compounds and knowledge about the reaction mechanisms have received considerable attention. Numerous variables affect the catalytic process, including metal–support interaction, metal particle sizes, and promoters. CO2 hydrogenation into different hydrocarbon compounds like lower olefins, alcoholic composites, long-chain hydrocarbon composites, and fuels, in addition to other categories, have been explained in previous studies. With respect to catalyst design, photocatalytic activity, and the reaction mechanism, recent advances in obtaining oxygenated hydrocarbons from CO2 processing have been made both through experiments and through density functional theory (DFT) simulations. This review highlights the progress made in the use of three-dimensional (3D) nanomaterials and their compounds and methods for their synthesis in the process of hydrogenation of CO2. Recent advances in catalytic performance and the conversion mechanism for CO2 hydrogenation into hydrocarbons that have been made using both experiments and DFT simulations are also discussed. The development of 3D nanomaterials and metal catalysts supported on 3D nanomaterials is important for CO2 conversion because of their stability and the ability to continuously support the catalytic processes, in addition to the ability to reduce CO2 directly and hydrogenate it into oxygenated hydrocarbons.

Theoretical study of small aromatic molecules adsorbed in pristine and functionalised graphene

Small aromatic molecules are precursors for several biological systems such as DNA, proteins, drugs, and are also present in several pollutants. The understanding of the interaction of these small aromatic molecules with pristine and functionalised graphene (fGr) can generate different applications. We performed ab initio simulations based on the density functional theory to evaluate the interaction between the aromatic compounds, benzene, benzoic acid, aniline and phenol, with pristine and fGr. The results show that the binding energy for all cases is less than 103.24 kJ/mol (1.07 eV) without substantial modification of the electronic properties, indicating that the interaction occurs through a physical adsorption regime. The results are promising because they suggest that pristine graphene and functionalised graphene are suitable for removing these pollutants, or for carrying molecules for biological applications influenced by π-π and H-bonds interaction.

Kinetic, equilibrium, and thermodynamic studies on the adsorption of ciprofloxacin by activated carbon produced from Jerivá (Syagrus romanzoffiana)

High specific surface area activated carbon prepared from endocarp of Jerivá (Syagrus romanzoffiana) (ACJ) was used for ciprofloxacin (CIP) antibiotic removal from aqueous effluents. The activated carbon (AC) was characterized via scanning electron microscope, Fourier transform infrared spectroscopy, N₂ adsorption/desorption, and pH value at the zero-charge point. Avrami kinetic model was the one that best fit the experimental results in comparison to the pseudo-first-order and pseudo-second-order kinetic models. The equilibrium data obeyed the Liu isotherm equation, showing a maximum adsorption capacity of 335.8 mg g^-1 at 40 °C. The calculated thermodynamic parameters indicate that the adsorption of CIP was spontaneous and endothermic at all studied temperatures. Also, the free enthalpy changes (∆H° = 3.34 kJ mol^-1) suggested physical adsorption between CIP and ACJ. Simulated effluents were utilized to check the potential of the ACJ for wastewater purification. The highly efficient features enable the activated carbon prepared from endocarp of Jerivá, an attractive carbon adsorbent, to remove ciprofloxacin from wastewaters.

Interactions of graphene derivatives with glutamate-neurotransmitter: A parallel first principles - Docking investigation

Glutamate plays an important role in excitatory neurotransmission, learning, and memory processes, and under pathological conditions it is directly associated with several chronic neurological disorders, such as depression, epilepsy, schizophrenia, and Parkinson's. Therefore, the detection and quantification of Glutamate is important for the rapid diagnosis of these diseases. Using first principles and molecular docking simulations we have evaluated the energetic, structural, and binding properties of graphene derivatives, such as pristine graphene (pristine-Gr) and oxidized graphene with carboxylic (Gr-COOH), carbonyl (Gr-COH), hydroxyl (Gr-OH), and epoxy (-O-) groups interacting with the glutamate neurotransmitter. The calculated binding affinity free energies from the docking complexes (glutamate-graphene family) suggest higher oxidized graphene-based glutamate molecular recognition than the pristine-Gr, with the following order of oxidized graphene derivatives according to ab initio results: (Gr-O∼Gr-COOH ∼ Gr-COH > Gr-OH)>pristine-Gr. Herein, the ab initio binding energies found for the glutamate-graphene family complexes are in the range of 0.24-0.80 eV. The configurations studied showed a biophysical adsorption regime without significant changes in the physico-chemical properties of the adsorbed glutamate neurotransmitter, in accordance with the general acceptance criteria of the detection systems.

The influence of the concentration and adsorption sites of different chemical groups on graphene through first principles simulations

Carbon nanomaterials are one of the most promising nanostructures for adsorption of chemical species due to their high superficial area and possible interesting applications. A systematic study of chemical groups attached on graphene surfaces is necessary in order to evaluate the influence of the type and number of functionalizations on the resulting properties of a derived system. In this work, first principles simulations were used to evaluate the physical effects of different concentrations of chemical groups -COOH, -COH, -OH, -O- or -NH₂ adsorbed on the graphene surface. The functionalizations occur from one up to three chemical groups and either in the same or different carbon rings. It is observed that significant changes occur in the adsorption and electronic properties due to the hybridization and symmetry points of interaction of the chemical groups. Then, the results indicate that it is possible to control the properties of the desired system through the type, concentration and binding site of the functional groups attached to the graphene monolayer.

Acridine orange adsorption by zinc oxide/almond shell activated carbon composite: Operational factors, mechanism and performance optimization using central composite design and surface modeling

Zinc Oxide/Activated Carbon Powder was used for the adsorptive removal of Acridine Orange dye (AO) from aqueous solution. The prepared composite material was characterized using XRD, XPS, SEM, EDS, FTIR, XRF, Raman, BET surface area and TGA/DTA. The adsorption isotherms, kinetics and thermodynamic studies of AO onto the ZnO-AC were thoroughly analyzed. The kinetic modeling data revealed that the adsorption of AO has a good adjustment to the pseudo-second-order model. Langmuir isotherm model is better fitted for adsorption data and the maximum adsorption capacity was found to be 909.1 mg/g at 313 K. The negative values of ΔG showed the spontaneous nature of the AO adsorption onto ZnO-AC. The results indicated the adsorption was pH dependent which is mainly governed by electrostatic attraction, hydrogen bonding and π-π interaction. Reusability test showed a low decrease in the removal performance of ZnO-AC due to the mesopore filling mechanism confirmed by BET analysis after adsorption. Also, thermal regeneration could deposit AO dye on the surface of the composite leading to the efficiency decrease. Finally, the effect of various parameters such as pH, temperature, contact time and initial dye concentration was studied using response surface methodology (RSM). The model predicted a maximum AO removal (99.42 ± 0.57%) under the optimum conditions, which was very close to the experimental value (99.32 ± 0.18%).

Adsorption of anti-inflammatory nimesulide by graphene materials: a combined theoretical and experimental study

Interactions of anti-inflammatory nimesulide with different graphene material species were explored employing both ab initio calculations and a batch adsorption process.

Coal fly ash/CoFe2O4 composites: a magnetic adsorbent for the removal of malachite green from aqueous solution

The removal efficiency for malachite green using CFA/CFO as adsorbent is significantly improved.