While Cheminformatics is formally a very old research field, building the foundations for Cheminformatics seen from the perspective of state-of-the-art theoretical Computer Science is not at all established research. Within Chemistry, many researchers speak of a revolution based on the deep understanding of Chemical Reaction Networks. However, conceptually new approaches for synthetic design and discovery of advantageous pathways are still to be developed. In our research approaches we promote modeling chemistry with algebraic graph rewriting approaches. In contrast to many other interdisciplinary fields within Cheminformatics, the atomic explicitness of such a modeling often allows for a direct application of results from theoretical Computer Science and graph theory.