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A systems theory for chemistry is proposed in order to provide a general framework, which covers different theoretical approaches used in the molecular sciences. The basic elements of systems theory are introduced and discussed. By construction, this systems chemistry offers classification and categorization schemes that will help to identify the range of applicability of certain theoretical approaches as well as to find yet unanswered fundamental questions. Consequently, it will be of value not only to those who want to understand and study the structure of chemistry, but it might also be of importance to daily research in chemistry.