Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

Dendronized vesicles: formation, self-organization of dendron-grafted amphiphiles and stability

Fundamental bacterial functions like quorum sensing can be targeted to replace conventional antibiotic therapies. Nanoparticles or vesicles that bind interfacially to charged biomolecules could be used to block quorum sensing pathways in bacteria. Towards this goal, dendronized vesicles (DVs) encompassing polyamidoamine dendron-grafted amphiphiles (PDAs) and dipalmitoyl-sn-glycero-3-phosphocholine lipids are investigated using the molecular dynamics simulation technique in conjunction with an explicit solvent coarse-grained force field. The key physical factors determining the stability of DVs as a function of the dendron generation and relative concentration are identified. The threshold concentration of each dendron generation that yields stable DVs is determined. Dendrons with lower generations rupture the DVs at high relative concentrations due to the electrostatic repulsions between the terminally protonated amines. Whereas, dendrons with intermediate generations demonstrate a mushroom-to-brush transition. Conformational changes in the dendrons expand the outer DV surface, resulting in instability in the DV bilayer. DVs encompassing dendrons with higher generations incur stresses on the bilayer due to their high charge density and spontaneous curvature. The self-organization of PDAs on the DV surface are examined to understand how the asymmetric stresses are minimized across the bilayer. A set of conditions are determined to be conducive for the formation of a single cluster of PDAs that decorates the DV surface like a mesh. Results from this study can potentially guide the design and synthesis of nanoparticles which target quorum sensing pathways in bacteria towards the prevention and treatment of bacterial infections. Furthermore, these nanoparticles can be used in diverse applications in biomedicine, energy or electronics that require synthetic dendronized cells or the adsorption and transport of charged species.

Synthesis, characterization and applications of poly-aliphatic amine dendrimers and dendrons

In the current era, the dendrimers have vast potential applications in the area of electronics, healthcare, pharmaceuticals, biotechnology, engineering products, photonics, drug delivery, catalysis, electronic devices, nanotechnologies and environmental issues. This review recaps the synthesis, characterization and applications of poly-aliphatic amine dendrimers.

A non-conjugated polyethylenimine copolymer-based unorthodox nanoprobe for bioimaging and related mechanism exploration

A non-conjugated polyethylenimine copolymer-based nanoprobe for lysosome-specific staining and tumor-targeted bioimaging and related mechanism exploration.

Removal of Cd(II) and Fe(III) from DMSO by silica gel supported PAMAM dendrimers: Equilibrium, thermodynamics, kinetics and mechanism

A series of silica gel supported amino-terminated PAMAM dendrimers (SG-G1.0 - SG-G3.0) were used for the removal of Cd(II) and Fe(III) from dimethylsulfoxide (DMSO). Various parameters that influence adsorption behaviors including temperature, contact time, and initial metal ion concentration were studied. The adsorption mechanism was revealed by combining the results of experiment and density functional theory (DFT) calculation. It indicates that the adsorption capacities for Cd(II) and Fe(III) are largest among the metal ions tested. The adsorption capacity of SG-G1.0 - SG-3.0 for Cd(II) and Fe(III) follows the order of SG-G2.0 > SG-3.0 > SG-G1.0. The adsorption isotherm shows the adsorption capacities for both metal ions increases with raising the temperature and initial metal ion concentration. The adsorption isotherm is consistent with Langmuir model and the adsorption process is dominated by chemical adsorption mechanism. Thermodynamic parameters indicates that the adsorption for both Cd(II) and Fe(III) is spontaneous and endothermic. Kinetic adsorption indicates that the adsorption equilibrium times for Cd(II) and Fe(III) is about 200 and 350 min, respectively, which can be described by a pseudo-second-order model and controlled by film diffusion process. FTIR analysis and theoretical calculation revealed that the carbonyl O atoms, secondary amine N atoms, and primary amine N atoms are the primary factor responsible for PAMAM adsorption by forming tetra- and penta-coordinated chelates with metal ions.

Charge and hydration structure of dendritic polyelectrolytes: molecular simulations of polyglycerol sulphate

Macromolecules based on dendritic or hyperbranched polyelectrolytes have been emerging as high potential candidates for biomedical applications. Here we study the charge and solvation structure of dendritic polyglycerol sulphate (dPGS) of generations 0 to 3 in aqueous sodium chloride solution by explicit-solvent molecular dynamics computer simulations. We characterize dPGS by calculating several important properties such as relevant dPGS radii, molecular distributions, the solvent accessible surface area, and the partial molecular volume. In particular, as the dPGS exhibits high charge renormalization effects, we address the challenges of how to obtain a well-defined effective charge and surface potential of dPGS for practical applications. We compare implicit- and explicit-solvent approaches in our all-atom simulations with the coarse-grained simulations from our previous work. We find consistent values for the effective electrostatic size (i.e., the location of the effective charge of a Debye-Hückel sphere) within all the approaches, deviating at most by the size of a water molecule. Finally, the excess chemical potential of water insertion into dPGS and its thermodynamic signature are presented and rationalized.

Mechanisms underlying interactions between PAMAM dendron-grafted surfaces with DPPC membranes

Biofouling is a pervasive problem which demands the creation of smart, antifouling surfaces. Towards this end, we examine the interactions between a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer and a polyamidoamine (PAMAM) dendron-grafted surface. In addition, we investigate the impact of dendron generation on the system behavior. To resolve the multiscale dynamical processes occurring over a large spatial scale, we employ Molecular Dynamics simulations with a coarse-grained implicit solvent force field. Our results demonstrate the transient and equilibrium system dynamics to be determined by the PAMAM dendron generation along with the underlying mechanisms. Higher generation dendrons are observed to favor penetration of the DPPC molecules into the dendron branches, thereby enabling sustained interactions between the membrane and the dendron-grafted surface. Under equilibrium, the membrane adopts a bowl-shaped morphology whose dimensions are determined by the dendron generation and density of interactions. The results from our study can be used to guide the design of novel surfaces with selective antifouling properties which can prevent the adsorption of microorganisms onto lipid membranes.

The interactions between a DPPC lipid membrane and a PAMAM dendron-grafted surface.