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At the 2006 IEEE International Conference on Systems of Systems Engineering, Boardman and Sauser presented a set of characteristics based on an integrative review of the literature. These characteristics are the foundation of the Boardman–Sauser system of systems (SoS) theory. We accept this theory as the basis of collaborative SoS and desire a means to validate this assertion. While numerous simulations have been published, the target SoS is usually a specific implementation. These specialized simulations produce results applicable primarily to the system under study but not necessarily SoS in general. Simulating the mathematical model of the Boardman–Sauser SoS theory in the form of an agent-based model produces results that can be compared with chemical reactions. This paper contends that the formation of molecules from atoms is an analog of systems forming any collaborative SoS, which we call our molecule organization model. The result is a supported logical argument that validates the Boardman–Sauser SoS theory as definitive of a generic SoS with behavior applicable to collaborative SoS. This paper seeks to provide a unique contribution to the SoS body of knowledge by increasing our understanding of collaboration in an SoS, so we may better understand their health, maintenance, replication, and evolution. [ABSTRACT FROM PUBLISHER]