Abstract
Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.
Highlights
Computer Assisted Structure Elucidation (CASE) of chemical compounds is one of the classical problems positioned at the intersection of informatics, chemistry, and mathematics
Structure generation from elemental formula The algorithm presented in this work, the Open Molecule Generator, was tested and compared with the commercial structure generator, MOLGEN
Our results show that the implementation of our algorithm generates all possible and valid chemical structures for a given elemental composition and optionally prescribed substructures
Summary
Computer Assisted Structure Elucidation (CASE) of chemical compounds is one of the classical problems positioned at the intersection of informatics, chemistry, and mathematics. CASE tools have been employed during decades to elucidate the chemical structure of small organic molecules. In its most general definition, a structure elucidation system receives experimental chemistry data of an unknown molecule as input, and outputs a list of possible chemical structures. The input can be the elemental composition of the elusive molecule, nuclear magnetic resonance (NMR) and/or mass spectrometry (MS) spectra (provided the generator can simulate spectra and match it to the experimental ones) or information of prescribed substructures. The output is a list of candidate structures matching these conditions, ideally containing all possible structures without duplications. The ultimate goal for such a system being fully automated and returning only one and correct molecule is not yet at our reach, despite decades of research [1]
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