Rhodium(III) complexes containing 9,10-phenanthrenequinone diimine (phi) ligands have been broadly applied for the construction of DNA binding and recognition molecules, and more recently, derivatives containing the 5,6-chrysenequinone diimine (chrysi) ligand have been shown specifically to recognize base mismatches in DNA. Here the structural properties of [Rh(bpy)(2)(chrysi)]Cl-3 and spectroscopic properties of derivatives are examined and compared to those of phi complexes of rhodium. Although similar in many respects, phi and chrysi complexes display distinctly different protonation behavior. The pK(a) values of chrysi complexes are as much as I unit lower than analogous phi compounds, and visible spectra of the chrysi complexes differ markedly from the phi counterparts in acidic but not basic solution. This protonation behavior is traced to the presence of a steric clash between a proton on the aromatic ring of the chrysi ligand and the acidic immino proton of the metal complex. In avoidance of this steric clash, a significant disruption in the planarity of the chrysi ligand is evident crystallographically in the structure of [Rh(bpy)(2)(chrysi)]Cl-3. 3CH(3)CN . 2H(2)O (triclinic crystal system, space group P (1) over bar (No. 2), Z = 2, a = 9.079(3) Angstrom, b = 10.970(3) Angstrom, c = 21.192(8) Angstrom, alpha = 86.71(3)degrees, beta = 89.21(3)degrees, gamma = 78.58(3)degrees, V = 2065.4(12) Angstrom(3)). Phi complexes, lacking the additional aromatic ring, require no similar distortion from ligand planarity. NMR spectra support this pH-dependent structural distortion for the chrysi complex. Rhodium complexes of chrysenequinone diimine, therefore, not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH "gated" ligand conformational switch.