Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set

Abstract

Peptoids are biomimetic materials in which the substituent groups are located on the nitrogen atom of the peptide bond, facilitating the formation of nanosheet structures as reported by Mannige et al. (Nature, 526 (2015) 415). Dissipative particle dynamics (DPD) simulations were performed to investigate the aggregation stability of peptoids with different unit lengths. The crucial effective interaction parameters were determined by fragment molecular orbital (FMO) calculations, which allowed to evaluate different molecular interactions (electrostatic and dispersion) in a balanced way. The experimental observation of the unit length dependence was finally reproduced by this FMO-DPD method.

Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method

“…Although PIEs of connected fragments are typically not used in the studies of the binding of macromolecules to ligands, their values may be used in topological models 49 of macromolecules and multiscale simulations. 50,51 For every bond at a fragment boundary in FMO, there is a bond detached atom (BDA) and a bond attached atom (BAA), see Figure 2.…”

Development of reverse mapping system bridging dissipative particle dynamics and fragment molecular orbital calculation

“…32) The scheme of DPD with FMO-derived χ parameters was named FMO-DPD, and it has been successfully applied to several systems. [33][34][35][36][37] These applications may indicate that FMO-DPD with FCEWS is reliable as a multiscale method from the nanoscale to the mesoscale. When the reverse mapping procedure from the mesoscale to the nanoscale is developed in conjunction with the FMO calculations for interaction analysis, the bidirectionality of FMO-DPD is realized.…”

DPD simulation to reproduce lipid membrane microdomains based on fragment molecular orbital calculations

“…Typically, these parameters are derived from experimental data or classical molecular mechanics (MM). 49,50) Alternatively, the parameters can be calculated using FCEWS, 51,52) a workflow system that uses the fragment molecular orbital (FMO) calculations 53,54) to reliably perform non-empirical DPD simulations 42,47,[55][56][57] (referred to as FMO-DPD). FCEWS could thus provide robust support for DPD simulations of unknown phenomena.…”