Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abbass, H., Wiggins, G., Lakshmanan, R., Morton, B.: Heat exchanger network retrofit by constraint logic programming. Computers in Chemical Engineering (1999)
Andersen, J., Flamm, C., Merkle, D., Stadler, P.: Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete. Journal of Systems Chemistry 3(1) (2012)
Benkö, G., Centler, F., Dittrich, P., Flamm, C., Stadler, B., Stadler, P.: A topological approach to chemical organizations. Artificial Life 15(1), 71–88 (2009)
Cook, A., Johnson, A.P., Law, J., Mirzazadeh, M., Ravitz, O., Simon, A.: Computer-aided synthesis design: 40 years on. WIREs Comput. Mol. Sci. 2, 79–107 (2012)
Corey, E.J.: General methods for the construction of complex molecules. Pure Appl. Chem. 14, 19–38 (1967)
de Moura, L., Bjørner, N.: Z3: An Efficient SMT Solver. In: Ramakrishnan, C.R., Rehof, J. (eds.) TACAS 2008. LNCS, vol. 4963, pp. 337–340. Springer, Heidelberg (2008)
Dittrich, P., Ziegler, J., Banzhaf, W.: Artificial chemistries - a review. Artificial Life 7(3), 225–275 (2001)
Flamm, C., Ullrich, A., Ekker, H., Mann, M., Hogerl, D., Rohrschneider, M., Sauer, S., Scheuermann, G., Klemm, K., Hofacker, I., Stadler, P.F.: Evolution of metabolic networks: A computational frame-work. Journal of Systems Chemistry 1(4) (2010)
Graph grammar library, http://www.tbi.univie.ac.at/~xtof/software/GGL/
Henry, C., Broadbelt, L., Hatzimanikatis, V.: Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnology and Bioengineering 106(3), 462–473 (2010)
Jiang, X., Meng, X., Xian, M.: Biosynthetic pathways for 3-hydroxypropionic acid production. Applied Microbiology and Biotechnology 82(6), 995–1003 (2009)
Kruger, N., von Schaewen, A.: The oxidative pentose phosphate pathway: structure and organisation. Current Opinion in Plant Biology 6(3), 236–246 (2003)
Kugler, H., Plock, C., Roberts, A.: Synthesizing Biological Theories. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 579–584. Springer, Heidelberg (2011)
Maris, A., Konings, W., Dijken, J., Pronk, J.: Microbial export of lactic and 3-hydroxypropanoic acid: implications for industrial fermentation processes. Metabolic Engineering 6(4), 245–255 (2004)
McNaught, A., Wilkinson, A.: IUPAC compendium of chemical terminology, vol 2. Blackwell Scientific Publications (1997)
Nelson, D., Cox, M.: Lehninger Biochemie. Springer (2005)
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M.: Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 27(1), 29 (1999)
Ranise, S., Tinelli, C.: The SMT-LIB standard: Version 1.2. Department of Computer Science, The University of Iowa, Tech. Rep. (2006)
Suthers, P., Cameron, D., et al.: Production of 3-hydroxypropionic acid in recombinant organisms. US Patent 6,852,517 (February 8, 2005)
Todd, M.H.: Computer-aided organic synthesis. Chem. Soc. Rev. 34, 247–266 (2005)
Willke, T., Vorlop, K.: Industrial bioconversion of renewable resources as an alternative to conventional chemistry. Applied Microbiology and Biotechnology 66(2), 131–142 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Fagerberg, R., Flamm, C., Merkle, D., Peters, P. (2012). Exploring Chemistry Using SMT. In: Milano, M. (eds) Principles and Practice of Constraint Programming. CP 2012. Lecture Notes in Computer Science, vol 7514. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33558-7_64
Download citation
DOI: https://doi.org/10.1007/978-3-642-33558-7_64
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-33557-0
Online ISBN: 978-3-642-33558-7
eBook Packages: Computer ScienceComputer Science (R0)