Polyethylene Surface Functionalization

This modifier functionalizes polyethylene (PE) surfaces by replacing selected CH2 units at the particle surface with CO, ester, or amide groups. Surface atoms are identified using the GITIM algorithm implemented in pytim [1] [2] on an MDAnalysis universe [3]. A random subset of eligible backbone carbons is chosen. End-group carbons are excluded.

Functionalization types

CO replaces CH2 with a carbonyl group.
``COH``replaces CH2 with a hydroxy group.
ester replaces CH2-CH2 with COO.
amide replace CH2-CH2 with CONH.

Modes

Random mode selects a target number of CH2 sites based on the requested percentage and then chooses positions at random while respecting neighbor_exclusion to keep functional groups separated. A neighbor_exclusion value of three means, that between two functional groups are at least three untouched CH2 units.

Command line

-funcPEsurf random:percentage:func_type:neighbor_exclusion

--functionalizePEsurface

Random functionalization of the PE surface by replacing CH2 groups with func_type.
func_type is CO, COH, ester, or amide.
percentage is a float from 0 to 100.
neighbor_exclusion is the minimum C-C hop distance between functional groups.

-funcPE-file

--functionalizePE-file

Output filename.

Default: functionalizedPE.xyz

Example

MakroLyzer -xyz PE.xyz -funcPEsurf random:15:CO:2 -funcPE-file PE_CO.xyz

Note

Chain-end carbons (with only one carbon neighbor) are excluded from functionalization.

Output

An XYZ file containing the modified structure.