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There is a lot of graph theory in Chemistry - modelling chemicals as (vertex/edge coloured) graphs, reaction networks, etc. Of course some molecules (eg aromat
by gilleain 4mo ago
There is a lot of graph theory in Chemistry - modelling chemicals as (vertex/edge coloured) graphs, reaction networks, etc.
Of course some molecules (eg aromatic systems, like ferrocene) are not naturally representable as graphs. I wonder if it is the same with synthesis - are there reactions hard to model as a graph (or petri net or whatever). One simple example I know is that you have to be careful with including a node for 'water' as it gets connected to everything else! Or at least in biochemistry it does.
- Obscurity4340 4mo agoWhy 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