Molecular dynamics simulations were carried out to investigate the structure of a gold‐nanoparticle including 169 Au atoms coated by 42 thiol terminated hydroquinonyl oligoether chains. Three nanoparticle systems were constructed and investigated for structural comparison. The simulation showed that in all three nanosystems thiol‐chains self‐assembled on the surface of the gold cluster to form a stable gold nanoparticle. The configurations of the thiol chains and stacking of the phenylene rings were analyzed. The thiol‐chains are bundled into groups. Each group contains no more than four chains, in which phenylene rings in the thiol‐chains are correlated in parallel and perpendicular forms. Simple quantum mechanical calculations are carried out to elucidate the correlation of the phenylene rings.
