Exploring Chemistry Using SMT

  • Rolf Fagerberg
  • Christoph Flamm
  • Daniel Merkle
  • Philipp Peters
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7514)


How to synthesize molecules is a fundamental and well studied problem in chemistry. However, computer aided methods are still under-utilized in chemical synthesis planning. Given a specific chemistry (a set of chemical reactions), and a specified overall chemical mechanism, a number of exploratory questions are of interest to a chemist. Examples include: what products are obtainable, how to find a minimal number of reactions to synthesize a certain chemical compound, and how to map a specific chemistry to a mechanism. We present a Constraint Programming based approach to these problems and employ the expressive power of Satisfiability Modulo Theory (SMT) solvers. We show results for an analysis of the Pentose Phosphate Pathway and the Biosynthesis of 3-Hydroxypropanoate. The main novelty of the paper lies in the usage of SMT for expressing search problems in chemistry, and in the generality of its resulting computer aided method for synthesis planning.


Reaction Mechanism Pentose Phosphate Pathway Vector Representation Rule Mapping Constraint Logic Programming 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Rolf Fagerberg
    • 1
  • Christoph Flamm
    • 2
  • Daniel Merkle
    • 1
  • Philipp Peters
    • 1
  1. 1.Department of Mathematics and Computer ScienceUniversity of Southern DenmarkDenmark
  2. 2.Institute for Theoretical ChemistryUniversity of ViennaAustria

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