Automated design of protecting molecules for metal nanoparticles by combinatorial molecular simulations

New tripod oligo(dibenzyl sulfide) molecules were designed by computer modeling calculations so that they would form 1:1 complexes with an Au147 nanoparticle. Twelve aromatic molecules containing two methylthiomethyl groups were used as construction units (“residues”). Combinations of the residues (“sequences”) were examined by molecular dynamic simulations, and those sequences giving the largest interaction energies with the gold nanoparticle were sought through either full search or genetic algorithm. Best-fit sequences were found for N = 5 and 6 (N is the number of “residues” in one leg of the tripod molecule).