As part of a conformation analysis of a library of piano stool complexes to find global minima and TS, a relaxed scan where the legs of the piano stool complex rotated about the Cp-M bond need to be performed (Here a $\ce{[(Me-Cp)RuClH(CO)]}$ is given here to illustrate the task in question) :

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However it was found that Gaussian 09 or 16 does not allow dummy atoms in redundant coordinates and cannot build dihedrals where one of the atoms is a dummy atom as far as Generalised Internal Coordinates (GIC) goes, because atoms are not considered an internal coordinate. Also unlike this question, since the rotation has to be done about the Cp-M bond,the workaround in that question will not work.

In addition, none of the existing dihedrals can be added together to give a dihedral where the middle bond will be aligned to the Cp-M axis. This means, the dummy atom for the centre of the Cp is necessary.

  1. What are the possible workarounds that can achieve an outcome equivalent to the relaxed scan of the Cp-M dihedral?

  2. Are there other chemistry packages that allow relaxed scan using dummy atoms or (better) user defined rotation axes?

  • $\begingroup$ I tried, I tried very hard. Even with the awesome possibilities of GIC, this does not work. You quickly surpass the number of imposable constraints when trying to fix an axis (and plane) and then use the arccos to scan the angle. The definition worked, but the scanning failed in predicting the next geometry. $\endgroup$ Jul 11 '18 at 17:44

I would use the dummy, define the 3 X 10 11 (16 and 18 too) dihedrals in the connectivity matrix, run the optimization and later write a shell script for running subsequent calculations in separate files replacing the value of the previously defined dihedrals. So I guess my solution is only slightly above doing it by hand but so far I haven't found any software that does this and G09 has no workaround.

I hope this helps


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