In dye-sensitized solar cells, three structurally similar dyes are commonly employed to sensitize anatase nanocrystals, namely, the cis-bis(isothiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato)-ruthenium(II) dye (N3) and its twice deprotonated (N719) and completely deprotonated (N712) forms. Using density functional theory, several possible binding geometries of these dyes are identified on the anatase(101) surface. Computed relative energies show that protonation of the surface can strongly influence the relative stabilities of these configurations and could induce a conformational transition from double bidentate-bridged binding to mixed bidentate/monodentate binding. Attenuated total reflection (ATR)-IR experiments and computed vibrational spectra provide additional support for a protonation-dependent equilibrium between two different configurations. Furthermore, self-assembly in chains of hydrogen-bonded dye molecules seems structurally favorable on the anatase(101) surface; for enantiopure dyes, a packing density of 0.744/nm² could be achieved.