2 ms·

> 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

by ElFitz 4mo ago

> 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/ https://pmc.ncbi.nlm.nih.gov/articles/PMC9574932/

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 ago
  Why is ferrocene ungraphable or in this context unable to be modelled in that way?
  - gilleain 4mo ago
    I 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 ago
      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 https://pubs.acs.org/doi/10.1021/acs.jcim.5c00265

by ElFitz 4mo ago

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 ago
Why is ferrocene ungraphable or in this context unable to be modelled in that way?
- gilleain 4mo ago
  I 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 ago
    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 https://pubs.acs.org/doi/10.1021/acs.jcim.5c00265