To understand the self-assembly process of the transition metal (TM) nanoclusters and nanowires self-synthesized by hydroquinone (HQ) and calix[4]hydroquinone (CHQ) by electrochemical redox processes, we have investigated the binding sites of HQ for the transition-metal cations TM(n+)=Ag(+), Au(+), Pd(2+), Pt(2+), and Hg(2+) and those of quinone (Q) for the reduced neutral metals TM(0), using ab initio calculations. For comparison, TM(0)-HQ and TM(n+)-Q interactions, as well as the cases for Na(+) and Cu(+) (which do not take part in self-synthesis by CHQ) are also included. In general, TM-ligand coordination is controlled by symmetry constraints imposed on the respective orbital interactions. Calculations predict that, due to synergetic interactions, silver and gold are very efficient metals for one-dimensional (1D) nanowire formation in the self-assembly process, platinum and mercury favor both nanowire/nanorod and thin film formation, while palladium favors two-dimensional (2D) thin film formation.