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We present a combined Raman–density functional theory (DFT) study of novel dipyridophenazine (dppz) derivatives and their Ru–bipyridine complexes. Our results show that the molecular architecture of dppz and its Ru complexes can be considered to consist of two independent moieties, the structural ground state properties of which can be tuned independently by means of side-specific substitution. These results are expected to be of importance for the design of highly specific dppz-based DNA sensors. Methodologically, the results presented in this paper highlight the power of a combined Raman–DFT approach to unravel the details of the structural properties of complex molecules.