Penetration of Chitosan into the Single Walled Armchair Carbon Nanotubes: Atomic Scale Insight

 

2. Materials and Methods 

2.1. Molecular Dynamics Simulations 

The non-reactive MD simulations were performed by means of GROMACS-5.1 (de-

veloped by University of Groningen, Royal Institute of Technology and Uppsala Univer-

sity) program package [32]. The armchair nanotubes 3D structures was created with nano-

tube builder which is one of the options of VMD software (version 1.9.2, University of 

Illinois at Urbana-Champaign, Champaign, IL, USA) (see Figure 1a,b) [33]. The three types 

of CNTs were created with the following parameters: CNT1(9:9), CNT2(11:11) and 

CNT3(13:13). In our simulations, we used three different model systems MOD1, MOD2 

and MOD3, which contains CNT1, CNT2 and CNT3, respectively. The length of the all 

CNT’s is the same, i.e., 3.26 nm, and the radii of the latter differs one to another. The hy-

drogen atoms were added to the terminal ends of the CNT using a Jmol software [34].