CHARMM force field for protonated polyethyleneimine.

Abstract

We present a revised version of our previously published atomistic Chemistry at Harvard Macromolecular Mechanics (CHARMM) force field for polyethyleneimine (PEI). It is based on new residue types (with symmetric CNC backbone), whose integer charges and bonded parameters are derived from ab initio calculations on an enlarged set of model polymers. The force field is validated by extensive molecular dynamics simulations on solvated PEI chains of various lengths and protonation patterns. The profiles of the gyration radius, end-to-end distance, and diffusion coefficient fine-tune our previous results, while the simulated diffusion coefficients excellently reproduce experimental findings. The developed CHARMM force field is suitable for realistic atomistic simulations of size/protonation-dependent behavior of PEI chains, either individually or composing polyplexes, but also provides reliable all-atom distributions for deriving coarse-grained force fields for PEI. © 2018 Wiley Periodicals, Inc.