Simulation of the intrinsic viscosity of hyperbranched polymers with varying topology. 1. Dendritic polymers built by sequential addition

pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules

The construction of a molecular topology file is a prerequisite for any classical molecular dynamics simulation. However, the generation of such a file may be very challenging at times, especially for large supramolecules. While many tools are available to provide topologies for large proteins and other biomolecules, the scientific community researching nonbiological systems is not equally well equipped. Here, we present a practical tool to generate topologies for arbitrary supramolecules: The pyPolyBuilder. In addition to linear polymer chains, it also provides the possibility to generate topologies of arbitrary, large, branched molecules, such as, e.g., dendrimers. Furthermore, it also generates reasonable starting structures for simulations of these molecules. pyPolyBuilder is a standalone command-line tool implemented in python. Therefore, it may be easily incorporated in persisting simulation pipelines on any operating systems and with different simulation engines. pyPolyBuilder is freely available on github: https://github.com/mssm-labmmol/pypolybuilder.

Dendrimer Dynamics: A Review of Analytical Theories and Molecular Simulation Methods

The theoretical study of dendrimers is reviewed, considering both analytical approaches and molecular simulation methods. We discuss the effect of molecular symmetry on the degeneracy of the relaxation times, and then the calculation of observable quantities, in particular the intrinsic viscosity, and then the viscoelastic complex modulus and the dynamic structure factor, in comparison with the available experimental data. In particular, the maximum intrinsic viscosity with increasing molar mass is analyzed in some detail. The approximations and/or assumptions of the adopted methods are also described in connection with analogous results for polymer of a different topology, in particular linear and star polymers.

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.

Molecular dynamics simulation studies of hyperbranched polyglycerols and their encapsulation behaviors of small drug molecules

Computer simulation could disclose more details about the conformations of HPGs and their encapsulation behaviors of guest molecules.

Recent developments and applications of bioinspired dendritic polymers

This review highlights the bioinspired applications of dendritic polymers, focusing on their structure–function relationship to natural biomolecules such as proteins.

Properties of aliphatic hyperbranched polyesters in dilute solutions

The results of an investigation of the influence of the synthesis procedure, number of pseudo generations and degree of branching of hydroxy-functional aliphatic hyperbranched polyesters (AHBP) on the values of limiting viscosity number, [?], hydrodynamic radius, R?, molar mass and polydispersity index, Q, are presented in this paper. Two series of AHBP, synthesized from 2,2-bis(hydroxymethyl) propionic acid and di-trimethylolpropane using a pseudo-one-step and a one-step procedure were investigated. The obtained results show that the values of [?] and R? for all examined samples are the highest in a 0.7 mass % solution of LiCl in N,N-dimethylacetamide (LiCl/DMAc), which indicates that this solvent is the best from the investigated ones. The values of [?] in N-methyl-2-pyrrolidinone (NMP) increased up to the sixth pseudo generation, after which a slight decrease occurred as the consequence of the presence of side-reaction products, formed during the synthesis. The appearance of these side-reaction products was also confirmed from the characteristic GPC chromatograms. For the samples of AHBP synthesized using the pseudo- one-step procedure, a good linear dependence between log [?] and log Mw was obtained up to the fifth pseudo generation, when LiCl/DMAc, NMP and DMAc were used as solvents. The values of the "shrinking" factor, g?, were calculated for all investigated AHBPs.

Structure characterization of hyperbranched poly(ether amide)s. I. Preparative fractionation

The focus of our investigation lies on the separation of typically broadly distributed hyperbranched poly(ether amide)s into narrow fractions of various molar masses. Their exact molar mass found via size-exclusion chromatography (SEC) with light uttering detection allows us to use these fractions for sample specific calibration in the SEC investigation of other hyperbranched samples. The analysis of the degree of branching, molar mass and viscosity behavior of the fractions gives a first indication about their molecular shape and the contribution of that shape to the overall viscosity. We determined the Mark-Houwink exponent for a hyperbranched sample using a number of narrow fractions which showed that an increase of molar mass leads to an increased molecular density.

Topological analysis of long-chain branching patterns in polyolefins

Patterns in molecular topology and complexity for long-chain branching are quantitatively described. The Wiener number, the topological complexity index, and a new index of 3-starness are used to quantify polymer structure. General formulas for these indices were derived for the cases of 3-arm star, H-shaped, and B-arm comb polymers. The factors affecting complexity in monodisperse polymer systems are ranked as follows: number of arms >> arm length > arm central position approximately equal to arm clustering > total molecular weight approximately equal to backbone molecular weight. Topological indices change rapidly and then plateau as the molecular weight of branches on a polyolefin backbone increases from 0 to 5 kD. Complexity calculations relate 2-arm or 3-arm comb structures to the corresponding 3-arm stars of equivalent complexity but much higher molecular weight. In a subsequent paper, we report the application of topological analysis for developing structure/property relationships for monodisperse polymers. While the focus of the present work is on the description of monodisperse, well-defined architectures, the methods may be extended to the description of polydisperse systems.

The Viscosity of Solutions of Poly(propylene imine) Dendrimers in Methanol

The viscosity of solutions of poly(propylene imine) dendrimers in methanol has been determined. An Ubbelohde and a low-shear rotational viscometer have been used. The viscosity was Newtonian for every concentration and shear rate used. The value of the Huggins coefficient indicates soft sphere behavior. The viscosity of the lower generations as a function of the volume fraction can be described with a single exponent, where the exponent is comparable to the intrinsic viscosity. The viscosity of the 4th and 5th generation dendrimers shows a stronger increase from a volume fraction of about 0.15 to 0.30. This increase is much smaller than that expected, using the Krieger-Dougherty formula for hard spheres with the hydrodynamic radius determined from the intrinsic viscosity. This smaller increase and the small value of the Huggins coefficient are interpreted in terms of a breakdown of the solvation layer. At a volume fraction of 0.3 the dendrimers, using the radius of gyration as the radius, start to touch each other. From the dependence of the viscosity on the concentration and the dependence of the viscosity on the molar weight, it can be concluded that dendrimers do not interpenetrate. It is concluded that they deform (collapse). Copyright 2001 Academic Press.