New directions in Regenerative Engineering and Nanotechnology Engineering require ab initio molecular design of intelligent molecular structures for advanced properties by controlling structure, recognition and specificity. This is the first step in coordinating and duplicating complex biological and physiological interactions associated with molecular recognition and targeting. We reexamine and further develop advanced, non-toxic, biocompatible biomaterials with sustainable characteristics. We use convergence with elements from biology, macromolecular chemistry and physics and non-ideal thermodynamic behavior to design novel structures. We use molecular models that establish the importance of molecular weight, degree of branching, swelling characteristics, thermodynamic compatibility and presence of “free” binding agents on the development of improved recognitive and targeting characteristics. Studies with thermodynamically intelligent biomaterials, branched structures, multi-arm polymers and gels indicate the importance of various molecular structures in Regenerative Engineering and Nanotechnology.