Molecular simulation study of PAMAM dendrimer composite membranes

Molecular dynamics simulation study of doxorubicin adsorption on functionalized carbon nanotubes with folic acid and tryptophan

In this work, molecular dynamics (MD) simulation is used to study the adsorption of the anticancer drug, doxorubicin (DOX), on the wall or surface of pristine and functionalized carbon nanotubes (FCNTs) in an aqueous solution. Initially, the CNTs were functionalized by tryptophan (Trp) and folic acid (FA), and then the DOX molecules were added to the system. The simulation results showed that the drug molecules can intensely interact with the FCNTs at physiological pH. Furthermore, it was found that as a result of functionalization, the solubility of FCNTs in an aqueous solution increases significantly. The effect of pH variation on drug release from both pristine and FCNTs was also investigated. The obtained results indicated that in acidic environments due to protonation of functional groups (Trp) and as a result of repulsive interaction between the DOX molecule and functional groups, the release of DOX molecules from FCNT’s surface is facilitated. The drug release is also strongly dependent on the pH and protonated state of DOX and FCNT.

Mechanism and Selectivity of Cyclopropanation of 3-Alkenyl-oxindoles with Sulfoxonium Ylides Catalyzed by a Chiral N,N'-Dioxide-Mg(II) Complex

The mechanism and stereoselectivity of an asymmetric cyclopropanation reaction between 3-alkenyl-oxindole and sulfoxonium ylide catalyzed by a chiral N,N'-dioxide-Mg(II) complex were explored using the B3LYP-D3(BJ) functional and the def2-TZVP basis set. The noncatalytic reaction occurred via a stepwise mechanism, with activation barriers of 21.6-23.5 kcal mol^-1. The C₂-C_α bond formed followed by the carbanion S_N2 substitution, constructing a three-membered ring in spiro-cyclopropyl oxindoles, accompanied by the release of dimethylsulfoxide. The electron-withdrawing N-protecting t-butyloxy carbonyl (Boc) and acetyl (Ac) groups in isatin enhanced the local electrophilicity of the C2 atom and the repulsion between the two COPh groups in the reactants, contributing to high reactivity as well as good diastereoselectivity results. The N-Boc-3-phenacylideneoxindole coordinated to the chiral ligand (L-PiPr₂) in a bidentate fashion, forming a hexacoordinate-Mg(II) complex as the reactive species. The origin of enantioselectivity was from the shielding effect of 2,6-diisopropylphenyl groups in the ligand toward the si-face of oxindole. The repulsion between the SO(CH₃)₂ and COPh groups in 3-alkenyl-oxindole and the neighboring ortho-iPr group in the ligand directed the re-face of ylide to attack the re-face of oxindole preferably, contributing to the high diastereoselectivity of the product. A metal-ion-ligand matching relationship was important for a good asymmetric induction effect of the chiral N,N'-dioxide-metal catalyst. A large chiral cavity in the Zn(II) catalyst weakened the shielding effect of 2,6-diisopropylphenyl groups in the ligand toward the prochiral face of oxindole, leading to inferior enantioselectivity observed in the experiment.

Coupled Monte Carlo and Molecular Dynamics Simulations on Interfacial Properties of Antifouling Polymer Membranes

We use molecular simulation to study the wetting behavior of antifouling polymer-tethered membranes. We obtain the interfacial properties (e.g., contact angle) of water at various temperatures for five polymer membranes, including a base polysulfone (PSF) membrane and four other PSF membranes grafted with antifouling polymers (two poly(ethylene glycol) (PEG) tethers and two zwitterionic tethers). We implement a coupled Monte Carlo (MC)/molecular dynamics (MD) approach to determine the interface potentials of water on the membrane surfaces in an efficient manner. Within this method, short MC and MD simulations are performed in cycles to collect the surface excess free energy of a thin water film on polymer membrane surfaces. Simulation results show that the grafting of zwitterionic tethers provides a more significant enhancement in the hydrophilicity of the PSF membrane than that of the PEG tethers. Water completely wets the surface of zwitterionic polymer membranes.

Investigation of nanoparticle-polymer interaction in bio-based nanosilica-filled PLA/NR nanocomposites: molecular dynamics simulation

Molecular dynamics (MD) simulation, by employing the COMPASS force field, was utilized to investigate structural and thermal characteristics as well as interfacial interactions between components of nanocomposite consisting of poly(lactic acid) (PLA)/natural rubber (NR)/nanosilica, abbreviated as PSxN, where 1 ≤ x ≤ 7 and it represents the parts of SiO₂ nanoparticles added to the PLA/NR (PN) blend. Analysis of the obtained results including density (ρ), fractional free volume (FFV), glass transition temperature (T_g), interaction energy (E_interaction), and radial distribution function (RDF) of these nanocomposites was performed. Comparing E_interaction of nanocomposites with that of the PN blend showed that the interactions between the chains of the two polymers are highly dependent on the added amounts of silica nanoparticles, so that by adding silica to the PN blend to obtain PS1N and PS3N nanocomposites, the amount of E_interaction was reduced to a smaller positive value, which indicates the tendency of the nanocomposite's components to interact with each other. By further addition of silica nanoparticles to have PS5N and PS7N nanocomposites and then by analysis of the RDF results, it was found that the nanoparticles were not well dispersed in these two nanocomposites and they were accumulated in the NR rubbery phase. Therefore, the percolation threshold for silica loading on the PN blend is at most 3 parts (x = 3). These results as well as the other obtained simulation results were compared with the available experimental data, and the agreement observed between them approved the simulation procedure and validated the obtained results.

Anomalous diffusion of polystyrene from an attractive substrate based on all-atom simulation

The diffusion of polystyrene (PS) polymer chains from a hydroxy (-OH)-terminated Si surface with different grafting densities φG is studied based on all-atom simulation. Our particular attention is paid to the impact of the attractive substrate on the diffusive and configurational properties of PS. Our simulation results uncover a very novel and unexpected modification to polymer diffusion with the increment of φG, namely, the diffusion is slowed down most significantly from a substrate with moderate grafting densities, while in lower or full grafting cases, the diffusive dynamics is even facilitated rather than retarded. The underlying mechanism is investigated in terms of energy and conformational change in detail. Surprisingly, we obtain a consistent scenario for diffusion. Under moderate grafting densities, the energy required to be overcome for diffusion is relatively large. In addition, PS chains are more likely to be in a stretched configuration subject to a slower relaxation. These facts can account for the hindered diffusion. While under lower or full grafting densities, the energy required for diffusion becomes even smaller than the ungrafted situation. Also, PS chains prefer a shrinking configuration undergoing faster relaxation. Consequently, the diffusion of PS is reasonably promoted.

Effect of pristine and functionalized single- and multi-walled carbon nanotubes on CO2 separation of mixed matrix membranes based on polymers of intrinsic microporosity (PIM-1): a molecular dynamics simulation study

Molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations were conducted to investigate the transport properties of carbon dioxide, methane, nitrogen, and oxygen through pure and mixed matrix membranes (MMMs) based on polymers of intrinsic microporosity (PIM-1). For this purpose, first, 0.5 to 3 wt% of pristine single-walled carbon nanotube (p-SWCNT) and multi-walled carbon nanotube (p-MWCNT) were embedded into the pure PIM-1, and then for better dispersion of CNT particles into the polymer matrix and to improve the performance of the resulting MMMs, polyethylene glycol (PEG) functionalized SWCNT and MWCNT (f-SWCNT and f-MWCNT, respectively) were loaded. The characterization of the obtained MMMs was carried out by using density, glass transition temperature, X-ray pattern, and fractional free volume calculations. Comparing the obtained results with the available reported experimental data, indicate the authenticity of the applied simulation approach. The simulation results exhibit that the pristine and PEG-functionalized CNT particles improve the transport properties such as diffusivity, solubility, and permeability of the PIM-1 membranes, without sacrificing their selectivity. Also, the MMMs incorporated with 2 wt% of the functionalized CNT particles indicate better performance for the CO₂ separation from other gases. According to the calculated results, the highest permeability and diffusivity for CO₂ are observed in the [PIM-1/f-SWCNT] MMM among the other membranes which represent that the loading of the f-SWCNTs can enhance the CO₂ separation performance of PIM-1 more than other CNTs studied in this work.

Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers

Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.