Self-assembly of single species polygons with patchy models in 2D

Abstract

The goal of this work is to produce single species of polygons in two dimensions using the self-assembly of a simple patchy molecular model. A molecule is defined as a central soft repulsive Weeks Chandler and Anderson (WCA) atom that is decorated with two or four patches, which describe the two models studied in this work. Model I has two Lennard–Jones (LJ) patches inside of its central atom separated by an angle θ that intends to define the number of polygon sides. The attractive potential of these patches, interacting as pairs, is used to bond molecules together to form polygons. Model II, having two additional soft repulsive WCA patches, tangent on the outside, produces single polygon species configurations. An example of Model I with an angle θ = 120 ∘ , forming a mixture of polygons, is included. Model II produces single polygon species with 3-8 sides, depending on the angle θ between the attractive patches. Molecular dynamics simulations in the canonical ensemble are used to calculate thermodynamic properties such as internal energy, percentage of polygons, pressure and contour plots for the percentage of polygons following isochoric processes. Different starting configurations are used to verify the consistency of the equilibrium results.