Structural Analysis and Simulation of Colloidal Clathrate Crystals Self Assembled from DNA-Functionalized Gold Nanoparticles

A recent paper [Lin et al., Science 2017] reported colloidal clathrate crystals self-assembled using programmable DNA-functionalized gold triangular bipyramids. Here, we present structural analysis of the experimental crystals and discrete element molecular dynamics simulations demonstrating their self-assembly. We show how the shape of the bipyramid can guide the DNA bonding to form a tetrahedral network, which is a common feature in clathrate formers. A minimal model in which a rigid bipyramid core is surrounded by a DNA shell is developed to simulate the assembly behavior. The DNA interaction between particles is represented by an effective pair potential where self-complementary hybridization and rounding effect are included. Our simulation results match well with the experimental observations, and we construct models to characterize structural properties of the experimental crystals.