It's been a while since I've studied chemistry. Now, I am reading the documentation of RDKit. At a certain point, the term "kekulization" is mentioned. What is kekulization (in RDKit, if this is not a standard chemical term)?
2 Answers
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This is a method to generate alternate Lewis structures of the same molecule. Here are two examples from the cumulative dissertation by Sascha Urbaczek[1]:
![Figure 2.1 (from [1]): Two examples for the ambiguities resulting from the description of molecules by valence bond structures. In case of asymmetric substitution at the aromatic ring, the two valence bond structures of example (1) are not identical due to the different locations of the double bonds. The same applies for the three structures in (2) in which both the double bond and the positive formal charge change positions.](https://i.stack.imgur.com/VaBTf.jpg)
If you were to search for the left molecule in panel (1) using an image search or a SMILES string, you might miss the right molecule in that panel.
According to the RDkit document cited in the question, the software routinely generates the alternate position of double bonds, and then (in a second step they call "aromatization") labels the ring as aromatic. In panel (2), there are three possible Lewis structures contributing to the actual structure (i.e. there is resonance), so the software would have to generate all three to be able to search for identical structures.
- Urbaczek, Sascha. A consistent cheminformatics framework for automated virtual screening. Ph.D. Thesis, Universität Hamburg, August 2014. URL: http://ediss.sub.uni-hamburg.de/volltexte/2015/7349/; URN: urn:nbn:de:gbv:18-73491; PDF via Semantic Scholar
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$\begingroup$ I do not really get the connection that led to the naming, but fwiw i suppose this is named after Kekulé? en.wikipedia.org/wiki/Kekul%C3%A9_Program $\endgroup$– bukwyrmJun 7, 2019 at 9:46
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2$\begingroup$ @bukwyrm Kekule of benzene structure fame. Alternate positions for double bonds, or delocalising the double bond electrons into hybrid orbitals. $\endgroup$– Neil_UKJun 7, 2019 at 13:25
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SMILES also exist in kekulized and non-kekulized forms. The kekulized form makes the double bonds in aromatic rings explicit. Instead, the normal (canonical) SMILES omits the double bond symbol = in favor of lowercase characters to denote aromaticity. For example:
Canonical SMILES:
CC(C)(C)c1cc(O)ccc1O
Kekulized:
CC(C)(C)C1=CC(O)=CC=C1O
