(176b) Amodeo: Automated Molecular Design Using Optimization

We describe and demonstrate a new software that automates, augments, and accelerates steps in computer-aided molecular design (CAMD). Our overall approach extends the scope of CAMD methods beyond group contribution models by employing accurate and extensive property models with a wide application domain. The molecular design 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 the relaxed design targets are identified. In the second stage, isomer structures of solution compositions are determined systematically and structure-based property corrections are utilized to refine the solution pool. In the final stage, the design is extended beyond the scope of group contribution methods by utilizing problem-specific property models. At each stage, optimization algorithms generate a large and diverse pool of candidate designs using an assortment of property models. The molecule generation machinery and external property models are bundled together to create an easy-to-use software.

The use of integer optimization techniques instead of enumeration at each stage, leads to an efficient algorithm, unrestricted in terms of the number of solutions sought and the maximum size of the molecule sought. Unique solutions are generated effectively with cuts to handle redundancy in chemical space. These optimization-based models lead to orders of magnitude decrease in solution time over enumeration or MINLP approaches. The software includes interfaces for external property models. The software also provides automated database searches and computational chemistry calculation options. We demonstrate the flexibility of the software using algebraic correlations, optimization-based models, and simulations as property estimation techniques.