Dithioether- or diamine-tethered adenine derivatives react with Pt-II, Pd-II, and Rh-III ions to give N3-coordinated complexes of the types [MCl(SSN)](+) (M = Pt or Pd), [RhCl3(SSN)], or [RhCl3(NNN)] (where SSN = 1-(N9-adenine)3,6-dithia-heptane or 1-(N9-adenine)-4,7-dithia-octane; NNN = ethylenediamine-N,9-ethyladenine). Single-crystal X-ray analysis confirms the nature of the metal-nucleobase interaction and highlights a conserved intermolecular hydrogen-bonding motif for all the complexes, irrespective of the metal-ion geometry. Coordination significantly reduces the basicity of the adeninyl group, as indicated by a pK(a) value of -0.16 for [PtCl(N3-1-(N9-adenine)-3,6-dithia-heptane)]BF4, compared to a pK(a) value of 4.2 for 9-ethyladenine. The site of proton binding, N1 or N7, could not be unambiguously assigned from the H-1 NMR data, because of the similar effect on the chemical shifts of the H2 and H8 protons. Density functional calculations at the BP-LACVP* level suggest N1 as the site of protonation for this type of complex. This is in contrast to the N7-protonation reported for [Pt(dien)(N3-6,6',9-trimethyladenine)](2+), as reported elsewhere (Meiser et al., Chem.-Eur. J. 1997, 3, 388). However, further electronic structure calculations in the gas phase reveal that the preferred site for protonation for N3-bound complexes is conformationally dependent. N3 coordination was also found to reduce the extent of base pairing between adenine and thymine in dimethylsulfoxide for the self-complementary complex [PtCl(L3)](+) (L3 = 1-(N9-adenine)-3,6-dithia-9-(N1-thymine)nonane), compared to that for the uncomplexed ligand.