Bastiaan van Hoorn, Patrick Norman and Mårten S. G. Ahlquist (2026)
Highlighted by Jan Jensen
Imagine if you could just draw a reaction in, say, ChemDraw, press a button, and get the TS (like shown above). Well now you pretty much can.**
Many algorithms construct TS guess structures by interpolating between reactant and product structures and therefore require that the atoms are in the same order. This can be very tedious to set up by hand and makes inclusion into automated workflows difficult.
In addition, I've found that the success of interpolation methods for biomolecular reactions depends heavily on how the reactant and product structures are aligned. Some methods try to solve this by rigid alignment, but that tends not to be sufficient for large, flexible molecules.
This paper offers automatic atom mapping and alignment, which is a massive step forward, in addition to a novel FF-based interpolation method that even includes some conformational sampling. And it works for "real-world" systems as you can see above.
Although VeloxChem can also optimise TSs, you can also interface it with other packages though a Python API. Here you can extract the interpolation path from VeloxChem (see this example notebook) and use that info (e.g. the TS guess or the aligned, atom-mapped reactant and product coordinates) as input to other packages if you want.
This is a really great tool that we are already using quite a bit in my group.
**You have to provide SMILES strings, which you can easily get from ChemDraw. For transition metal complexes (TMCs) you have to give (non-mapped) coordinates instead, because VeloxChem uses RDKit. ChemDraw can't produce RDKit-compatible SMILES for TMCs (but Schrödinger Sketcher can). Also, the 3D structures that RDKit produces for TMCs are not very good. However, my group and others are working on fixing this, so that should be available soon.
This work is licensed under a Creative Commons Attribution 4.0 International License.
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