Simulating self-assembly of porphyrin nanorods

Diacid meso-tetra(4-sulfonatophenyl)porphine (TPPS$_{4}^{2-}$ ) monomers have been shown to self assemble into nanorods with well-defined cross-section$^{1}$ and intriguing photoelectronic properties$^{2}$. However, the structure and conduction mechanism of these nanorods is poorly understood, and questions remain about the aggregation process. Using density functional theory (DFT), we first obtain optimized geometries and atomic-charges for the monomers, which we then use for subsequent molecular dynamics (MD) simulations to observe the initial stages of the self-assembly process. This work uses the resources of the National Energy Research Scientific Computing Center. $^{1}$A.D. Schwab \textit{et al.}, J. Phys. Chem. B \textbf{107}, 11339 (2003). $^{2}$A.D. Schwab \textit{et al.}, Nano Letters \textbf{4}, 1261 (2004).