A structural and thermodynamical characterization of complexation of poly(amidoamine) dendrimers with metal ions, metal atoms, and copper hydrates is carried out using ab initio (Hartree-Fock and density functional theory) techniques. Three binding sites (core, amide, and amine) are identified and the binding energies for attachment of naked Cu(II), Pt(II), Au(III), and Ag(I), as well as those of Cu, Pt, Au, and Ag to each of these sites are reported for PAMAM GO-NH2. Metal ions are tetracoordinated to the core site atoms, and three types of ion-amide site coordination are found: tetracoordinated for Ag(I), tridentate for Pt(II) and bidentate for Cu(II) and Au(III). A cooperative effect between amide and amine sites is found in the bidentate coordination of ions to amide and amine N atoms; for the metal atoms such coordination becomes monodentate (to the amine N). Metal atoms form bidentate (Pt, Cu, Ag), or monodentate (Au) complexes to the core and amide sites. A Cu(II) ion solvated with one water molecule retains its bidentate coordination to the amide site while keeping its strong interaction with the water oxygen, whereas a slightly weaker binding complex is formed between doubly hydrated Cu(II) and one of the amide oxygen atoms. The thermodynamics of Cu(II) hydration by 1 to 10 water molecules is compared with those of displacement complexation reactions where Cu2+ in various degrees of hydration reacts with a GO-NH2 dendrimer in gas phase.