Significant Improvement in CO2 Absorption by Deep Eutectic Solvents as Immobilized Sorbents: Computational Analysis.

To find an alternative way for improving the efficacy of deep eutectic solvents (DESs) to dissolve carbon dioxide, a computational study of DES systems comprising choline chloride and different hydrogen-bond donors (ethylene glycol and glycerol) immobilized on hydrophobic (graphite) and hydrophilic (titanium dioxide) solid surfaces was performed. This research provides quantitative molecular understanding of the role of the DES thickness and also the type of solid support in CO2 sorption and diffusion using molecular dynamics simulations. In general, the proposed model based on supported DESs immobilized on different supports was developed to correlate the solubility of CO2 in DESs based on choline chloride. The simulated systems illustrate that CO2 molecules mainly accumulate at the gas/DES interface in short times, whereas diffusion of CO2 to the bulk DESs is slower as the thickness of the immobilized DES increases. In addition, the CO2 absorption capacity of both DESs coated on the TiO2 surface is larger than that on the graphite surface. Structural and dynamic characteristics were determined using density profiles, distribution functions, orientational analysis, and mean-square displacements. We further demonstrate the effective interaction parameters associated with CO2 capture by DESs via density functional theory.

Synthesis of some new distyrylbenzene derivatives using immobilized Pd on an NHC-functionalized MIL-101(Cr) catalyst: photophysical property evaluation, DFT and TD-DFT calculations.

In this study the catalytic application of a heterogeneous Pd-catalyst system based on metal organic framework [Pd-NHC-MIL-101(Cr)] was investigated in the synthesis of distyrylbenzene derivatives using the Heck reaction. The Pd-NHC-MIL-101(Cr) catalyst showed high efficiency in the synthesis of these π-conjugated materials and products were obtained in high yields with low Pd-contamination based on ICP analysis. The photophysical behaviors for some of the synthesized distyrylbenzene derivatives were evaluated. The DFT and TD-DFT methods were employed to determine the optimized molecular geometry, band gap energy, and the electronic absorption and emission wavelengths of the new synthesized donor-π-acceptor (D-π-A) molecules in the gas phase and in various solvents using the chemical model B3LYP/6-31+G(d,p) level of theory.

The interactions of folate with the enzyme furin: a computational study.

Entrance of coronavirus into cells happens through the spike proteins on the virus surface, for which the spike protein should be cleaved into S1 and S2 domains. This cleavage is mediated by furin, a member of the proprotein convertases family, which can specifically cleave Arg-X-X-Arg↓ sites of the substrates. Here, folate (folic acid), a water-soluble B vitamin, is introduced for the inhibition of furin activity. Therefore, molecular insight into the prevention of furin activity in the presence of folic acid derivatives is presented. To this aim, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were performed to clarify the inhibitory mechanism of these compounds. In this regard, molecular docking studies were conducted to probe the furin binding sites of folic acid derivatives. The MD simulation results indicated that these drugs can efficiently bind to the furin active site. While the folic acid molecule tended to be positioned slightly towards the Glu271, Tyr313, Ala532, Gln488, and Asp530 amino acids of furin at short and long ranges, the folinic acid molecule interacted with Glu271, Ser311, Arg490, Gln488, and Lys499 amino acids. Consequently, binding free energy calculations illustrated that folic acid (-27.90 kcal mol-1) has better binding in comparison with folinic acid (-12.84 kcal mol-1).

Aqueous solutions of binary ionic liquids: insight into structure, dynamics, and interface properties by molecular dynamics simulations and DFT methods.

The behavior of aqueous solutions of mixtures of ionic liquids (ILs) is of special interest because of their amphiphilic character, from both a fundamental and application viewpoint. In this work, we conducted molecular dynamics (MD) simulations and density functional theory (DFT) calculations to understand the effect of water on the intermolecular interactions in three IL binary mixtures [C4mim]/[Cl]/[BF4], [C4mim]/[Cl]/[PF6] and [C4mim]/[BF4]/[PF6] containing the well-characterized cation, 1-n-butyl-3-methylimidazolium [C4mim]+ and the anions chloride [Cl]-, tetrafluoroborate [BF4]-, and hexafluorophosphate [PF6]-. The perturbation of the structures in the binary IL mixture by water molecules was analyzed in the bulk and at the liquid/vacuum interface using distribution functions, hydrogen-bond statistics, and density profiles. Interactions between anions and cations change drastically when the IL mixtures are dissolved in water. In particular, anion-water interactions are stronger than anion-cation interactions. H-Bonds are the dominant interactions. They are prevalently electrostatic and strong for the two [Cl]-containing systems in both the water-free and the water-containing systems. The very hydrophobic [C4mim]/[BF4]/[PF6] system gains stability from dispersive interactions and consequently segregates water markedly when admixed. The most probable orientations of IL cations in the bulk and at the vicinity of the interface were examined using bivariate distribution calculations and show [PF6]- segregating to the surface in keeping with its highly hydrophobic nature. DFT calculated structures, energies, dipole moments, global hardness and solvation energies using model ion pairs [C4mim][X] or complexes [C4mim]2[X][Y], with [X/Y]- = [Cl]-, [BF4]-, or [PF6]- are completely consistent with the findings for the bulk.

New insight into electrosynthesis of ordered TiO2 nanotubes in EG-based electrolyte solutions: combined experimental and computational assessment.

To obtain a better understanding of TiO2 nanotube (TiO2-NT) synthesis in different ethylene glycol (EG)-based electrolyte solutions by electrochemical anodization, the primary steps of TiO2-NT formation were studied by experimental techniques. In this regard, three different EG-based electrolyte solutions were used for anodic oxidation of titanium foil. The first electrolyte solution contains conventional ammonium fluoride (NH4F) dissolved in EG/water (98 : 2 v/v). In the second one, Ti foil anodization is performed in an electrolyte solution containing the 1-butyl-3-methyl-imidazolium tetrafluoroborate (Bmim-BF4) ionic liquid. Finally, the fluorine-containing species was replaced by the 1-butyl-3-methyl-imidazolium chloride (Bmim-Cl) ionic liquid. The results indicate that the TiO2-NTs did not form by anodization in the EG/H2O/Bmim-Cl electrolyte solution at 60 V. Interestingly, this electrolyte solution is less viscous than the fluorine-containing electrolyte solutions. In addition, we report a detailed study on the structural arrangement of electrolyte solution components near the solid surfaces using molecular dynamics (MD) simulation methods to reveal the factors governing the difference of the ionic species distribution. The MD results elucidate the role of the ionic constituents in the length of the nanotube arrays at a certain anodization condition. Furthermore, as reported herein for the first time, the lifetimes of ion-ion contacts and the interactions of ionic species with TiO2 walls have a substantial effect on the resulting nanotubes. These characteristics are analyzed by using radial distribution functions, density profiles, distance analysis, time correlation functions, and mean-square-displacements, complemented by DFT calculations.

The interactions of an Aß protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances.

Recent studies have shown that the aggregation of the amyloid-beta peptide (Aß) in the brain cell membrane is responsible for the emergence of Alzheimer's disease (AD); the exploration of effective factors involved in the extension of the aggregation process and alternatively the examination of an effective inhibitor via theoretical and experimental tools are among the main research topics in the field of AD treatment. Therefore, in this study, we used all-atom molecular dynamics (MD) simulations to clarify the impact of cell membrane cholesterol on the interaction of Aß with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a membrane model. Moreover, the effect of the P7C3-S243 molecule on the abovementioned process was investigated. The simulation results disclosed the neuroprotective property of the P7C3-S243 molecule. The MD simulation results indicate that the interaction of cholesterol molecules with the Aß oligomer is negligible and cannot enhance membrane rupture. However, strong hydrogen bonding between the POPC molecules and the oligomers led to membrane perturbation. According to our modellings, the P7C3-S243 molecular layer can protect the cell membrane by inhibiting the direct interaction between the bilayer and Aß. In addition, free-energy calculations were conducted to determine the possible penetration of Aß fibrils into the cholesterol-enriched membrane.

Confinement of aqueous mixtures of ionic liquids between amorphous TiO2 slit nanopores: electrostatic field induction.

Electrostatic potential in the vicinity of the surface is induced when aqueous mixtures of hydrophobic and hydrophilic ionic liquids (ILs) are confined between a slit nanopore of amorphous but not crystalline TiO2 semiconductors. According to our molecular dynamics (MD) simulations, the extent of ion-pairing lifetime under such nanoscale confinement is substantially lower than its value in the bulk. It becomes still lower when aqueous mixtures of ionic liquid electrolytes are used. Ion-ion correlation is broken completely in the confined dilute aqueous electrolyte systems. The anions and cations of the ILs migrate and accumulate at the opposite amorphous TiO2 electrodes that are separated by 10 nm to arrange a nanosize pore. In contrast, we have shown that the electrostatic interactions between the IL ions are dominant when the electrolyte is confined between anatase (101) TiO2. A similar trend is observed for the inorganic electrolyte system. These findings shed light on the design of new cells for electrochemical applications.

How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption?

Molecular dynamics (MD) simulations are conducted to suggest a mechanism of action for the aminopropyl dibromocarbazole derivative (P7C3) small molecule, which protects neurons from apoptotic cell death. At first, the influence of embedded Aß42 stacks on the structure of membrane is studied. Then, the effect of P7C3 molecules on the Aß42 fibril enriched membrane and Aß42 fibril depleted membrane (when Aß42 fibrils are originally dissolved in the aqueous phase) are evaluated. Also, the formation of an amyloid ion channel in the Aß42 enriched membrane is examined by calculating deuterium order parameter, density profile, and surface thickness. For Aß42 in the fully inserted state, ion channel-like structures are formed. The presence of P7C3 molecules in this case just postpones membrane destruction but could not prevent pore formation. In contrast, when both Aß42 and P7C3 molecules are embedded in the aqueous solution, the P7C3 molecules are self-assembled at membrane/ionic aqueous solution interface and prevent the precipitation and deposition of Aß42 fibrils into the membrane.