[ElFitz]

> Feels complex like solving a Rubik's cube to write down synthesis steps but it is all a sequence of memorized tricks. Do Cannizaro if you want this, Bergmann to do that.

I remember two years ago, when I actually got into using graph data structures, wondering if maybe the "space" of available reactions for any given starter and target molecules could be mapped as a graph, with intermediates as nodes and reactions as weighted directed edges, so synthesis becomes pathfinding through chemical space.

Turns out, it’s a thing! [^0]

Edit: Makes you wonder how much interesting stuff is sitting in plain sight, waiting for someone with the right cross-domain awareness / knowledge / whatever to notice it.

[0]: https://pmc.ncbi.nlm.nih.gov/articles/PMC9574932/

[gilleain]

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]

Why is ferrocene ungraphable or in this context unable to be modelled in that way?

[gilleain]

I meant metallocenes in general:

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]

From 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