Hybrid coarse-grained/atomistic model of “chitosan + carbon nanostructures” composites

Abstract

We present a new hybrid molecular dynamics model of chitosan oligomers which is constructed specifically for studying chitosan + carbon nanostructures composites, their structure and mechanical properties. The model is derived for application within the modified molecular mechanics force field AMBER. Method of virtual sites mapping allowed to retain hexagonal rings of chitosan backbone. Mass and structural disposition of virtual atoms has been found as function of joined groups' atoms masses and coordinates. Geometrical parameters (e.g., bond length, valence angles, torsional angles and van der Waals distances) were found using semi-empirical methods. Parameters of interaction within the AMBER force field were estimated according to structural and energy characteristics of chitosan dimers and oligomers. Model has successfully passed multilevel verification based on comparison of its behaviour with atomistic chitosan within the same force field. It appeared that the model reproduces structural and energy characteristics of chitosan and its composites with carbon nanostructures. Moreover, it allows estimation of their mechanical properties. Dynamical characteristics of composite components are also well reproduced.

Effect of Monomer Sequence and Degree of Acetylation on the Self-Assembly and Porosity of Chitosan Networks in Solution

“…Here, we use our coarse-grained model of chitosan to investigate how the sequence of GlcNAc monomers affects chitosan self-assembly in solution, the structure of the resulting hydrogel network, and the ability of molecules to diffuse within the network. To the best of our knowledge, the effect of monomer sequence on chitosan self-assembly has not been discussed previously in experimental − ,,, or simulation , studies. Thus, we do not believe that there are any experimental methods of controlling the sequence of GlcNAc monomers.…”

Development of a Coarse-Grained Model of Chitosan for Predicting Solution Behavior

“…26 This model uses a total of 7 spheres to represent each GlcN monomer, and is parameterized to accurately represent the interactions between chitosan and carbon nanostructures such as graphene nanoparticles and carbon nanotubes. 26 The atomistic simulations used to derive the hybrid model were performed in AMBER, but Coulomb interactions were neglected because the carbon nanostructures are not charged. 26 The authors found that the total molecular energies resulting from the atomistic and coarse-grained models differed by less than 1%, and the bulk densities of the chitosan molecules in the atomistic and coarse-grained models differed by less than 5%.…”

“…26 The atomistic simulations used to derive the hybrid model were performed in AMBER, but Coulomb interactions were neglected because the carbon nanostructures are not charged. 26 The authors found that the total molecular energies resulting from the atomistic and coarse-grained models differed by less than 1%, and the bulk densities of the chitosan molecules in the atomistic and coarse-grained models differed by less than 5%. 26 Marrink and coworkers have developed a more general way to coarse-grain carbohydrates by extending the MARTINI force field.…”

“…26 The authors found that the total molecular energies resulting from the atomistic and CG models differed by less than 1%, and the bulk densities of the chitosan molecules in the atomistic and CG models differed by less than 5%. 26 Marrink and coworkers have developed a more general method for coarsegraining carbohydrates by extending the MARTINI force field. 27 Monomers are broken into three CG sites, and the interaction potentials are assigned based on the four main types of interaction sites: polar (P), nonpolar (N), apolar (C), and charged (Q).…”

Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films

“…Petrov et al employed density functional theory (DFT) and DFT-based tight-binding to determine crystal structure configurations and hydrogen-bonding of chitin from a first-principles approach. On the other end of the multiscale methods, Yu and Lau have developed a coarse-grained model for chitin, allowing the simulation of 300 nm long chitin chains, while Kossovich et al , have developed a hybrid atomistic/coarse-grained model for chitosan, allowing simulations of 200 nm long chitosan chains. Recent studies − have also performed conformational and interaction analysis of chitosan with carbon nanotubes in aqueous solution for applications in drug delivery and structural reinforcement.…”