Polydopamine and eumelanin models in various oxidation states

We report a comprehensive ab initio structural investigation of more than 43 000 probable molecular structures of polydopamine (PDA) and eumelanin in various oxidation states. With the aid of a computational approach including a brute-force algorithmic generation of chemical isomers and density functional theory, all probable oxidized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically generated and evaluated. We identify a set of the most stable molecular structures of PDA and eumelanin which represent the chemically diverse nature of these materials. Results show that more planar molecular structures have a tendency to be more stable. We also observe that, in some cases, forming cyclic molecular structures could reduce the energy of a DHI tetramer and make it more stable. This finding supports the hypothesis that cyclic molecules could exist in eumelanin-like materials. Additionally, the cyclic molecular models proposed in this work are energetically more favorable than the popular porphyrin-like models in this field.