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Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data
Department of Mathematics and Computer Science, University of Southern Denmark, Odense M DK-5230, Denmark
Max Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany
Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
Institute for Theoretical Chemistry, University of Vienna, Wien A-1090, Austria
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig D-04107, Germany
Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, D-04103, Germany
Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C DK-1870, Denmark
Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe NM 87501, USA
* Author to whom correspondence should be addressed.
Received: 22 February 2013; in revised form: 10 September 2013 / Accepted: 11 September 2013 / Published: 25 September 2013
Abstract: Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a means of exploring the chemical spaces of HCN polymerization and hydrolysis. A fundamental issue is to understand the combinatorial explosion inherent in large, complex chemical systems. We demonstrate that experimental data, here obtained by mass spectrometry, and computationally predicted free energies together can be used to guide the exploration of the chemical space and makes it feasible to investigate likely pathways and chemical motifs even in potentially open-ended chemical systems.
Keywords: hydrogen cyanide; graph grammars; chemical space; mass spectrometry; chemical motif; polymerization; autocatalysis
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Andersen, J.L.; Andersen, T.; Flamm, C.; Hanczyc, M.M.; Merkle, D.; Stadler, P.F. Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy 2013, 15, 4066-4083.
Andersen JL, Andersen T, Flamm C, Hanczyc MM, Merkle D, Stadler PF. Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy. 2013; 15(10):4066-4083.
Andersen, Jakob L.; Andersen, Tommy; Flamm, Christoph; Hanczyc, Martin M.; Merkle, Daniel; Stadler, Peter F. 2013. "Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data." Entropy 15, no. 10: 4066-4083.