Brownian Dynamics Simulation of Hyperbranched Polymers under Elongational Flow

Molecular Dynamics of Lysine Dendrigrafts in Methanol-Water Mixtures

The molecular dynamics method was used to study the structure and properties of dendrigrafts of the first and second generations in methanol-water mixtures with various volume fractions of methanol. At a small volume fraction of methanol, the size and other properties of both dendrigrafts are very similar to those in pure water. A decrease in the dielectric constant of the mixed solvent with an increase in the methanol fraction leads to the penetration of counterions into the dendrigrafts and a reduction of the effective charge. This leads to a gradual collapse of dendrigrafts: a decrease in their size, and an increase in the internal density and the number of intramolecular hydrogen bonds inside them. At the same time, the number of solvent molecules inside the dendrigraft and the number of hydrogen bonds between the dendrigraft and the solvent decrease. At small fractions of methanol in the mixture, the dominant secondary structure in both dendrigrafts is an elongated polyproline II (PPII) helix. At intermediate volume fractions of methanol, the proportion of the PPII helix decreases, while the proportion of another elongated β-sheet secondary structure gradually increases. However, at a high fraction of methanol, the proportion of compact α-helix conformations begins to increase, while the proportion of both elongated conformations decreases.

Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.

Why the Orientational Mobility in Arginine and Lysine Spacers of Peptide Dendrimers Designed for Gene Delivery Is Different?

New peptide dendrimer with Lys-2Arg repeating units was recently studied experimentally by NMR (RSC Advances, 2019, 9, 18018) and tested as gene carrier successfully (Int. J. Mol. Sci., 2020, 21, 3138). The unusual slowing down of the orientational mobility of 2Arg spacers in this dendrimer was revealed. It has been suggested that this unexpected behavior is caused by the Arg-Arg pairing effect in water, which leads to entanglements between dendrimer branches. In this paper, we determine the reason for this slowing down using atomistic molecular dynamics simulation of this dendrimer. We present that the structural properties of Lys-2Arg dendrimer are close to those of the Lys-2Lys dendrimer at all temperatures (Polymers, 2020, 12, 1657). However, the orientational mobility of the H-H vector in CH2-N groups of 2Arg spacers in Lys-2Arg dendrimer is significantly slower than the mobility of the same vector in the Lys-2Lys dendrimer. This result is in agreement with the recent NMR experiments for the same systems. We revealed that this difference is not due to the arginine-arginine pairing, but is due to the semiflexibility effect associated with the different contour length from CH2-N group to the end of the side arginine or lysine segment in spacers.

Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers

In this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation was performed by molecular dynamics method in a wide range of temperatures. We have shown that the Lys-2Lys dendrimer has a larger size but smaller fluctuations as well as lower internal density in comparison with the Lys-2Gly dendrimer. The Lys-2Lys dendrimer has larger charge but counterions form more ion pairs with its NH 3 + groups and reduce the bare charge and zeta potential of the first dendrimer more strongly. It was demonstrated that these differences between dendrimers are due to the lower flexibility and the larger charge (+2) of each 2Lys spacers in comparison with 2Gly ones. The terminal CH 2 groups in both dendrimers move faster than the inner CH 2 groups. The calculated temperature dependencies of the spin-lattice relaxation times of these groups for both dendrimers are in a good agreement with the experimental results obtained by NMR.

Lysine Dendrigraft Nanocontainers. Influence of Topology on Their Size and Internal Structure

Poly-l-ysine dendrigrafts are promising systems for biomedical applications due to their biodegradability, biocompatibility, and similarity to dendrimers. There are many papers about the use of dendrigrafts as nanocontainers for drug delivery. At the same time, the number of studies about their physical properties is limited, and computer simulations of dendrigrafts are almost absent. This paper presents the results of a systematic molecular dynamics simulation study of third-generation lysine dendrigrafts with different topologies. The size and internal structures of the dendrigrafts were calculated. We discovered that the size of dendrigrafts of the same molecular weight depends on their topology. The shape of all studied dendrigrafts is close to spherical. Density profile of dendrigrafts depends on their topology.

NMR studies of excluded volume interactions in peptide dendrimers

Peptide dendrimers are good candidates for diverse biomedical applications due to their biocompatibility and low toxicity. The local orientational mobility of groups with different radial localization inside dendrimers is important characteristic for drug and gene delivery, synthesis of nanoparticles, and other specific purposes. In this paper we focus on the validation of two theoretical assumptions for dendrimers: (i) independence of NMR relaxations on excluded volume effects and (ii) similarity of mobilities of side and terminal segments of dendrimers. For this purpose we study 1H NMR spin-lattice relaxation time, T1H, of two similar peptide dendrimers of the second generation, with and without side fragments in their inner segments. Temperature dependences of 1/T1H in the temperature range from 283 to 343 K were measured for inner and terminal groups of the dendrimers dissolved in deuterated water. We have shown that the 1/T1H temperature dependences of inner groups for both dendrimers (with and without side fragments) practically coincide despite different densities of atoms inside these dendrimers. This result confirms the first theoretical assumption. The second assumption is confirmed by the 1/T1H temperature dependences of terminal groups which are similar for both dendrimers.

Self-Assembly of Lysine-Based Dendritic Surfactants Modeled by the Self-Consistent Field Approach

Implementing a united atom model, we apply self-consistent field theory to study structure and thermodynamic properties of spherical micelles composed of surfactants that combine an alkyl tail with a charged lysine-based dendritic headgroup. Following experiments, the focus was on dendron surfactants with varying tail length and dendron generations G0, G1, G2. The heads are subject to acetylation modification which reduces the charge and hydrophilicity. We establish a reasonable parameter set which results in semiquantitative agreement with the available experiments. The critical micellization concentration, aggregation number, and micelle size are discussed. The strongly charged dendronic surfactants micelles are stable for generation numbers G0 and G1, for progressively higher ionic strengths. Associates of G2 surfactants are very small and can only be found at extreme surfactant concentration and salt strengths. Micelles of corresponding weaker charged acetylated variants exist up to G2, tolerate significantly lower salt concentrations, but lose the spherical micelle topology for G0 at high ionic strengths.

HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user's specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

Elongation flow-triggered morphology transitions of dendritic polyethylene amphiphilic assemblies: host-guest implications

The assemblies and transformations of dendritic polyethylene (DPE)-poly(oligo(ethyleneglycol) methacrylate) (POEGMA) amphiphilic micelles have been demonstrated by cryo-TEM and DLS techniques under elongation flow stimuli. The flow rate-dependence of the dissymmetry ratio suggests the possibility that a combination of shear and elongation could also be responsible for the transitions of DPE-POEGMAs, but it is obvious that the exposure of elongation flow is essential and plays a key role in the assembly and fusion of the DPE-POEGMA micelles. Fluorescence resonance energy transfer (FRET) is used to provide insight into the assembly and fusion of DPE-POEGMA under elongation flow. The FRET results show that a shorter separation distance of DiO-DiI with higher elongation rate can result in higher FRET efficiency. Furthermore, DPE-POEGMAs can display the responsive switching ability of the elongation flow-triggered FRET.

Mechanochemistry of Topological Complex Polymer Systems

Although existing since the concept of macromolecules, polymer mechanochemistry is a burgeoning field which attracts great scientific interest in its ability to bias conventional reaction pathways and its potential to fabricate mechanoresponsive materials. We review here the effect of topology on the mechanical degradation of polymer chains and the activation of mechanophores in polymer backbones. The chapter focuses on both experimental and theoretical work carried out in the past 70 years. After a general introduction (Sect. 1), where the concept, the history, and the application of polymer mechanochemistry are briefly described, flow fields to study polymer mechanochemistry are discussed (Sect. 2), results of mechanochemistry study are presented for linear polymers (Sect. 3), cyclic polymers (Sect. 4), graft polymers (Sect. 5), star-shaped polymers (Sect. 6), hyperbranched polymers and dendrimers (Sect. 7), and systems with dynamic topology (Sect. 8). Here we focus on (1) experimental results involving the topological effect on the coil-to-stretch transition and the fracture of the polymer chains, (2) the underlying mechanisms and the key factor that determines the mechanical stability of the macromolecules, (3) theoretical models that relate to the experimental observations, and (4) rational design of mechanophores in complex topology to achieve multiple activations according to the existing results observed in chain degradation.

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).

Where are the End-Groups in a Hyperbranched Polymer?

The location of the end-groups in hyperbranched polymers is modelled by considering two synthetic strategies. The first synthesis is to make linear chains, and then link these chains. The second strategy is to sequentially add multifunctional monomers. The first strategy represents hyperbranched polymers synthesized by living radical methods, whereas the second represents polycondensations at low conversion. The high-conversion case is also considered. The present analysis suggests that sequential addition of monomers places more end-groups at the polymer’s surface than synthesis by linking chains. If the end-groups are catalysts, synthesis by the addition of monomers should give fewer inaccessible catalysts.

Models for randomly hyperbranched polymers: Theory and simulation

We derive theoretical models for the structures of randomly hyperbranched polymers in solution, and test them against computer simulations. The models are based on the same basic approach: Building a structure by the random assembly of "simple units," which may be monomers, linear chains, or larger branched species. Comparisons to simulation reported here show that the conformations of hyperbranched species, i.e., their radii of gyration and full density profiles, are accurately described by this approach. These stringent tests complement previous tests against experiment. We include the effects of solvent quality at the mean-field level. Our model works best for hyperbranched structures, but also reproduces very well the simulated density profiles of dendrimers. The models reported here provide a simple, but realistic, picture of the physical influences that affect the conformations of hyperbranched species.