Martini coarse‐grained model for polyethylenimine

Abstract

As a polycation with diverse applications in biomedical and environmental engineering, polyethylenimine (PEI) can be synthesized with varying degrees of branching, polymerization, and can exist in different protonation states. There have been some interests in molecular modeling of PEI at all‐atom or coarse‐grained (CG) levels, but present CG models are limited to linear PEIs. Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model branched PEIs. The CG model was developed under the Martini scheme based on eight ~600 Da PEIs, with four different degree of branching at two different protonation states. Comparison of the CG model with all‐atom simulations shows good agreement for both local (distributions for bonded interactions) and global (end‐to‐end distance, radius of gyration) properties, with and without salt. Compatibility of the PEI model with other CG bio‐molecules developed under the Martini scheme will allow for large‐scale simulations of many PEI‐enabled processes. © 2018 Wiley Periodicals, Inc.

Erratum: “Martini Coarse‐Grained Model for Polyethylenimine” [J. Comput. Chem. 2019, 40, 607–618, DOI:10.1002/jcc.25747]

“…Errors are reported and corrected below, and their consequences on the results are discussed. The model presented in our original article [ 1 ] is still deemed to be of good quality; in fact, all bonded parameters remain unchanged after the correction. Meanwhile, the model can be further improved by suggesting a change to the bead type for the uncharged polyethylenimine (PEI) beads.…”

“…Below references [2‐8] correspond to references [55], [67], [66], [61], [58], [56] and [63] respectively in the original article. [ 1 ]…”

“…Following the Martini methodology [ 2 ] , the bead type for uncharged PEI beads was determined in our original article [ 1 ] by considering a) the hydration free energy of the molecular analogue, ethylamine; and b) the partitioning free energy of ethylamine between water and different organic solvents. Marrink et al [ 2 ] provided the partitioning free energies of Martini beads “between water and a number of organic phases”, which should be interpreted as the free energy required to move a bead from organic solvent to water.…”

“…There is a difference in the sign convention for the partition free energy evaluation by Marrink et al [ 2 ] as compared to Duffy et al [ 4 ] and Abraham et al [ 3 ] . The errors in our original article [ 1 ] were partly due to misunderstanding of the difference in sign convention, and partly due to an arithmetic error while calculating the free energy to move ethylamine from hexadecane to water.…”

“…Following the same notations as in our original article [ 1 ] , Δ G hyd , , and are respectively the hydration free energy of a solute, and the partitioning free energy to move the solute from hexadecane (H), chloroform (C) and octanol (O) to water (W). These definitions are consistent with Marrink et al [ 2 ] , and were calculated using Equations ) at 300 K. For ethylamine, log P (water/gas) and log P (octanol/gas) were from Table 4 of Duffy et al [ 4 ] , log P (hexadecane/gas) was from Table 3 of Duffy et al [ 4 ] , and log P chl was from Table 2 of Abraham et al [ 3 ] Only experimental data was used, which was referred to as “exptl” in Duffy et al [ 4 ] and “obsd” in Abraham et al [ 3 ] …”