Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

Engineering surface patterns on nanoparticles: New insights on nano-bio interactions

The surface properties of nanoparticles affect their fates in biological systems. Based on nanotechnology and methodology, pioneering works have explored the effects of chemical surface patterns on the behavior of...

The branching angle effect on the properties of rigid dendrimers studied by Monte Carlo simulation

We studied the properties of rigid dendrimers with different branching angles by means of Monte Carlo simulations on a coarse-grained level. It was found that the terminal groups of dendrimers with both rigid and flexible spacers could locate near the center of the molecule. In flexible dendrimers, the wide distribution is attributed to the back folding of flexible spacers, while in rigid dendrimers, it is caused by the branching angle effect that a branch will grow laterally due to the restriction of a non-zero branching angle. It has been established that the branching angle is a key parameter for rigid dendrimers, which can be applied to tune the properties of rigid dendrimers: decreasing branching angle is helpful to obtain dendrimers with a larger size, lower density, and more terminal groups locating at periphery.

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.

Successive outermost-to-core shell directionality of the protonation of poly(propyl ether imine) dendritic gene delivery vectors

The protonation behaviour of polycationic compounds has direct relevance to their ability to condense and deliver nucleic acids. This report pertains to a study of the protonation behaviour of polycationic poly(propyl ether imine) (PETIM) dendritic gene delivery vectors that are constituted with tertiary amine core moiety and branch sites, n-propyl ether linkages, and primary amine peripheries. The ability of this series of dendrimers to condense nucleic acids and mediate endosomal escape was studied by unravelling the protonation behaviour of the dendrimers aided by pH metric titrations and 1H and 15N NMR spectroscopies. The results demonstrate protonation of the primary and tertiary amines of outermost-to-core shells occurring in a successive stepwise fashion, in contrast to other polycationic vectors. Theoretical calculations based on the Ising model rationalize further the finer details of protonation at each shell. The protonation pattern correlates with the endosomal buffering and nucleic acid condensation properties of this PETIM-based dendritic gene delivery vectors. The study establishes that the protonation behaviour is a critical and essential parameter to assess the gene condensation and delivery vector properties of a polycationic compound.

PAMAM dendrimer: a pH-controlled nanosponge

Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).

One-pot synthesize of dendritic hyperbranched PAMAM and assessment as a broad spectrum antimicrobial agent and anti-biofilm

Hyperbranched poly(amidoamine) (h-PAMAM) compound was synthesized from diethylene triamine and different moles percent of methyl acrylate using simple one-pot and commercial synthesis method. The synthesized h-PAMAM was provided with ester and amine terminations. Chemical structure of the synthesized h-PAMAM, with different terminations, was confirmed by Fourier Transform Infrared (FTIR) spectroscopy. In addition, the size and the distribution of the synthesized h-PAMAM were evaluated using Dynamic Light Scattering (DLS) analysis. The molecular weights of the synthesized modified hyperbranched polymer, with different terminations, were measured using Gel-permeation chromatograph. The ill-structure of the h-PAMAM with different molar feed methyl acrylate:diethylene triamine (MA:DETA) ratios was designed as h-PAMAM-amine, h-PAMAM-ester and h-PAMAM-amine plus (sharing similar chemical and physical properties with well-defined poly(amidoamine) (PAMAM) dendrimers in generation 2, 2.5 or 3, respectively). Moreover, the synthesized compound expressed broad spectrum antimicrobial and anti-biofilms activity.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Combined EPR and molecular modeling study of PPI dendrimers interacting with copper ions: effect of generation and maltose decoration

Understanding the early onset of neurodegeneration is crucial to deploy specific treatments for patients before the process becomes irreversible. Copper has been proposed as a biomarker for many neurodegenerative disorders, being the ion released by pathologically unfolded proteins involved in many biochemical pathways. Dendrimers are macromolecules that bind metal ions with a large ion/ligand ratio, thus, allowing a massive collection of copper. This work provides structural information, obtained via molecular modeling and EPR, for the binding sites of copper in polypropyleneimine (PPI) dendrimers, especially in the maltose decorated form that has potential applications in diagnosis and therapies for various types of neurodegenerations. The analysis of the EPR spectra showed that, at the lowest Cu concentrations, the results are well supported by the calculations. Moreover, EPR analysis at increasing Cu(II) concentration allowed us to follow the saturation behavior of the interacting sites identified by the modeling study.

A new microscopic insight into membrane penetration and reorganization by PETIM dendrimers

Dendrimers are highly branched polymeric nanoparticles whose structure and topology, largely, have determined their efficacy in a wide range of studies performed so far. An area of immense interest is their potential as drug and gene delivery vectors. Realizing this potential, depending on the nature of cell surface-dendrimer interactions, here we report controlled model membrane penetration and reorganization, using a model supported lipid bilayer and poly(ether imine) (PETIM) dendrimers of two generations. By systematically varying the areal density of the lipid bilayers, we provide a microscopic insight, through a combination of high resolution scattering, atomic force microscopy and atomistic molecular dynamics simulations, into the mechanism of PETIM dendrimer membrane penetration, pore formation and membrane re-organization induced by such interactions. Our work represents the first systematic observation of a regular barrel-like membrane spanning pore formation by dendrimers, tunable through lipid bilayer packing, without membrane disruption.

Theoretical and computational studies of dendrimers as delivery vectors

It is a great challenge for nanomedicine to develop novel dendrimers with maximum therapeutic potential and minimum side-effects for drug and gene delivery. As delivery vectors, dendrimers must overcome lots of barriers before delivering the bio-agents to the target in the cell. Extensive experimental investigations have been carried out to elucidate the physical and chemical properties of dendrimers and explore their behaviors when interacting with biomolecules, such as gene materials, proteins, and lipid membranes. As a supplement of the experimental techniques, it has been proved that computer simulations could facilitate the progress in understanding the delivery process of bioactive molecules. The structures of dendrimers in dilute solutions have been intensively investigated by monomer-resolved simulations, coarse-grained simulations, and atom-resolved simulations. Atomistic simulations have manifested that the hydrophobic interactions, hydrogen-bond interactions, and electrostatic attraction play critical roles in the formation of dendrimer-drug complexes. Multiscale simulations and statistical field theories have uncovered some physical mechanisms involved in the dendrimer-based gene delivery systems. This review will focus on the current status and perspective of theoretical and computational contributions in this field in recent years. (275 references).

End-group distributions of multiple generations of spin-labeled PAMAM dendrimers

Dendrimers are attractive templates to display functional molecular components. Since the behavior of dendrimer systems can depend greatly on the accessibility of these molecular components to the external environment, and on the spatial arrangement of functional groups attached to the dendrimer terminal branches (end-groups), techniques to determine the locations of end-groups are highly desirable. In this report, we describe a method to analyze the EPR spectra of multiple generations of poly(amidoamine) (PAMAM) dendrimers which have spin-labels attached to end-groups in variable percentages of the total number of available sites. The spectra are treated as a convolution of a narrow spin-label spectrum and a variable line broadening function. Trends in the parameters that describe the best-fit line broadening function with spin-label loading reveal the spatial arrangements and homogeneity of spin environments of the labels. We observe a shift in the end-group distribution from generation 3 (G(3)) to G(4) dendrimers that indicates a change in morphology from an open, extended structure to a more dense, compact arrangement.

Structure of polyamidoamide dendrimers up to limiting generations: a mesoscale description

The polyamidoamide (PAMAM) class of dendrimers was one of the first dendrimers synthesized by Tomalia and co-workers at Dow. Since its discovery the PAMAMs have stimulated many discussions on the structure and dynamics of such hyperbranched polymers. Many questions remain open because the huge conformation disorder combined with very similar local symmetries have made it difficult to characterize experimentally at the atomistic level the structure and dynamics of PAMAM dendrimers. The higher generation dendrimers have also been difficult to characterize computationally because of the large size (294,852 atoms for generation 11) and the huge number of conformations. To help provide a practical means of atomistic computational studies, we have developed an atomistically informed coarse-grained description for the PAMAM dendrimer. We find that a two-bead per monomer representation retains the accuracy of atomistic simulations for predicting size and conformational complexity, while reducing the degrees of freedom by tenfold. This mesoscale description has allowed us to study the structural properties of PAMAM dendrimer up to generation 11 for time scale of up to several nanoseconds. The gross properties such as the radius of gyration compare very well with those from full atomistic simulation and with available small angle x-ray experiment and small angle neutron scattering data. The radial monomer density shows very similar behavior with those obtained from the fully atomistic simulation. Our approach to deriving the coarse-grain model is general and straightforward to apply to other classes of dendrimers.

Structural Elucidation of Dendritic Host–Guest Complexes by X-ray Crystallography and Molecular Dynamics Simulations

The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The results from the two methods are consistent and suggest a preferred molecular picture of this complicated aggregate of multiple components. The guest molecules can bind to the dendrimer in a variety of ways although most involve hydrogen-bonding interactions between urea groups of the dendrimer with urea and/or carboxylic acid groups of the guest. In addition, acid-base interactions between the carboxylic acid of the guest and the tertiary amine in the interior of the dendritic host are present. Our proposed structure gives important information about the predominant dynamic interactions between the host and guest and illustrates how they fit together and interact with each other.