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

Abstract

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.

A functional hyperbranched binder enabling ultra-stable sulfur cathode for high-performance lithium-sulfur battery

“…Fully atomistic simulations are conducted with Gromacs 4.5.4 MD software package by using OPLS-AA force field [42 , 43] . All Starting coordinates of the investigated structures are produced by the in-house software HBP Builder [44] . Then the initial structures are subjected to 50 0 0 steps for steepest descent minimization of the potential energy.…”

stk: A python toolkit for supramolecular assembly

“…It is therefore useful to be able to automate the construction of a large number of polymers and oligomers from monomer building blocks and to then evaluate their performance for a given application through computational screening. While tools for building polymers already exist they are often specialized and work as standalone software. This means that integrating them into diverse workflows is more difficult and that experience using one tool cannot be used to build other supramolecular classes in the future.…”

Practical computational toolkits for dendrimers and dendrons structure design

“…This is particularly true for larger generations or for non-regular dendrimers or dendrons with complex structures. Several molecular modelling tools are suited to build regular dendrimers and hyper-branched polymers, namely Starmaker (part of Silico toolkit) [36,37], Dendrimer Building Toolkit [30], Dendrimer Builder in Materials Studio [38] and HBP builder [39]. However, there are still opportunities to automate process of generation of the structures of more complex dendrimers or dendrons.…”

“…Our toolkit is not suited for the generation of random copolymers, hyperbranched polymers with random branching and dendrigrafts. These features can be found in molecules builders available in Material Studio or HBP [39] and therefore those resources should be used instead.…”