Greetings Frank Schaper

I have personally used the Chemcraft software for a similar task, it lets you open two windows with similar structures and automatically match, reorder the atomic captions and generate new xyz files (it might not be intuitive, but it is possible to do it quickly). Otherwise, I think you could look for similar features in other molecular viewers/editors.

Regarding the "averaged" position, you might want to read a little bit into the NEB TS searching, it is available in the ORCA quantum chemistry package and it is, sometimes, an affordable way to search for transition states using two local minima (even though, it is just another way for finding a TS, and not a way to circunvent the match/reordering).

Hello Frank Schaper

In addition to a great answer from Lucas Gian Fachini, I suggest you try out the "connection editor" of GaussView.

You open the structures of your rotamers in a single window and use the connection editor to match the numbers automatically or manually (sometimes! It is unavoidable. In my case, methyl groups). There, you will find multiple options to renumber; this can also help you get a good starting z-matrix (optimization in internal coordinates is generally better than in cartesian coordinates).

A quick way to get a TS guess is to interpolate between two structures; I use interpolation in internal coordinate or geodesic interpolation code (https://github.com/virtualzx-nad/geodesic-interpolate/tree/master). The latter code implements the method described in the paper " Geodesic interpolation for reaction pathways." You may need to write a custom code to extract information from the output.

I hope this helps.

Regards,

Dilawar

there are various software tools available for structure matching and renumbering atoms, such as rdkit, open babel, and pymol.

Hello Frank Schaper

If you prefer to calculate an "averaged" structure from the aligned structures, you can manually average the coordinates of corresponding atoms using scripting or programming languages such as Python. However, be aware that this approach may not always produce meaningful results, especially if the structures have significant differences in conformation or geometry.

To align two structures with different atom numbering/ordering, you can use structural alignment software or molecular visualization tools that support structure superposition and alignment. Here are some options: PyMOL, VMD (Visual Molecular Dynamics), Chimera, Open Babel,...

Once you have aligned the two structures using one of these tools, you can proceed with your QST2 transition state search in Gaussian using the aligned structures.