2 ms·
Why is ferrocene ungraphable or in this context unable to be modelled in that way?
by Obscurity4340 4mo ago
Why is ferrocene ungraphable or in this context unable to be modelled in that way?
- gilleain 4mo agoI meant metallocenes in general: https://en.wikipedia.org/wiki/Metallocene https://en.wikipedia.org/wiki/Metallocene A metal atom sandwiched between two Cp rings. You _can_ model this as 5 single bonds between each atom of a ring (so 10 total C-M bonds), or you have to have some kind of 'edge' (bond) between the ring as a whole and the metal. The more general issue is that a graph model of a chemical assumes a 'bond' is between exactly two atoms. Three-center hydrogen bonds are another example where this model fails to capture the chemistry very well. Of course, it's a tradeoff - you can model _most_ compounds with just graphs (plus atom type, charge, chirality) and the relatively few that do not quite fit are special cases.
- ElFitz 4mo agoFrom what I found, current state of the art on modelling "reaction space" with graphs that is to use "hypergraphs" where edges can lead to more than one node[^0]. But I am just someone who got curious; not even an amateur ^^’ [0]: https://pubs.acs.org/doi/10.1021/acs.jcim.5c00265 https://pubs.acs.org/doi/10.1021/acs.jcim.5c00265