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In chemical biology, there is a large demand for molecular tools that allow a measurement or manipulation of biological systems. Such technologies can help to understand biochemical processes of living organisms as well as to develop medical therapies or methods for biotechnology. Recently, bond-breaking reactions were added to this chemical biology toolbox, in addition to the well established bond-forming ligation reactions like the clickreaction. A protecting group can be removed as a consequence of a bond cleavage (uncaging), restoring thereby the original compound and its initial biological/chemical/physical activity. For some time, these uncaging reactions were limited to photoreactive groups. In more recent work it was shown that it is possible to perform such an activation reaction not just with the aid of light but also with molecular actors in a so called chemical activation. In the course of this uncaging the bond cleavage can occur either in a stoichiometric way with organic molecules or catalytically with a metal complex. For such a bioorthogonal, catalytic uncaging reaction the group of E. Meggers has been developing potent catalyst-substrate-pairs consisting of ruthenium complexes and alloc-protected amines since 2006. In the beginning of the dissertation at hand, it is discussed how the catalytic efficiency of the ruthenium complexes developed by E. Meggers could be further optimized through ligand modifications. The new complexes of the type [CpRu(R-HQ)(allyl)]PF6 (HQ = 8-Hydroxyquinolinate) and especially the 5-methyl ester derivative showed the highest efficiency in the uncaging of alloc-protected amine substrates. As a result, a 7-fold greater turnover number and a 3-fold increase in the turnover frequency was achieved under biologically relevant conditions. The 5-methyl ester complex is not just the most productive but also with a rate constant k2 of 580 m−1s−1 the fastest metal catalyst for chemical activation. The complex reached a high activity not only in aqueous solution but also in blood serum and in human cell cultures. Besides different fluorophores the anti-cancer drug doxorubicin was also uncaged, resulting in a 10-fold reduction of cellular viability. For the optimization of the catalytic efficiency and bioorthogonality not just the ligand scaffold was modified but also selected complexes were implemented into macrostructures like proteins, nanoparticles or the cellular lipid membrane. In addition, the development of stimulus responsive complexes is presented at the end of this work. On the one hand, a photoreactive complex is described which is inactive under physiological conditions and only under exposure to light is able to turn over substrates. On the other hand, the concept of a complex is discussed that can be switched by the proton concentration, resulting for example in the possibility to measure the pH value of biological systems.