A new framework to automate, augment, and accelerate steps in computer-aided molecular design is presented. The problem is tackled in three stages: (1) composition design, (2) structure determination, and (3) extended design. Composition identification and structure determination are decoupled to achieve computational efficiency. Using approximate group-contribution methods in the first stage, molecular compositions that fit design targets are identified. In the second stage, isomer structures of solution compositions are determined systematically, and structure-based property corrections are used to refine the solution pool. In the final stage, the design is extended beyond the scope of group-contribution methods by using problem-specific property models. At each design stage, novel optimization models and graph theoretic algorithms generate a large and diverse pool of candidates using an assortment of property models. The wide applicability and computational efficiency of the proposed methodology are illustrated through three case studies. (c) 2013 American Institute of Chemical Engineers AIChE J, 59: 3686-3701, 2013