How to know the distance of Cp-M or Arene-M?

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dkratzert
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Re: How to know the distance of Cp-M or Arene-M?

Post by dkratzert » 14 Apr 2018, 17:32

I just realized that SHELXL has a nice possibility to calculate the distance of an atom to the centroid of a ring with error. It even calculates the centroid position automatically:

SHELXL manual:
RTAB codename atomnames
"[...] If the codename is D2CG, the distance of the first atom to the unweighted centroid of the remaining atoms is calculated (with esd). This is useful for finding distances to mid-points of cyclopentadiene rings for example."

For a gallium atom over a benzene ring:

RTAB D2CG Ga1 C20 C21 C22 C23 C24 C25

Result in the list file:

Distances from first atom to centroid of a group of atoms (D2CG) and x,y,z of centroid
2.6039 (0.0026) Ga1 - [ C20 C21 C22 C23 C24 C25 ] 0.75657 0.45206 0.23510

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markoru
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Re: How to know the distance of Cp-M or Arene-M?

Post by markoru » 14 Apr 2018, 19:07

Yes, this nice option in SHELXL is available since v. 2014/1 and coordinates of the centroid are listed since v. 2017/1. This should be the best way to calculate such a distance, for it includes properly determined esd.

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Helge
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Re: How to know the distance of Cp-M or Arene-M?

Post by Helge » 18 Apr 2018, 15:12

Thank you very much for mentioning this here! I would never have realised. And I am quite disturbed by the significant difference between the distance calculated by SHELXL (1.761) and by Diamond (1.730) in my latest structure with such a pi-complex.

dkratzert
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Re: How to know the distance of Cp-M or Arene-M?

Post by dkratzert » 18 Apr 2018, 15:16

That is indeed an astonishing difference. I also made the observation that distances calculated by Diamond are mostly c.r.a.p.

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markoru
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Re: How to know the distance of Cp-M or Arene-M?

Post by markoru » 19 Apr 2018, 20:57

Hm, although I don’t use Diamond, I wonder what might have caused such difference. I suspect that centroid calculated by Diamond doesn’t have same coordinates as one calculated by SHELXL (maybe there is some weighting scheme involved in Diamond algorithm for centroids calculation). Could you verify that? BTW, Mercury does calculations correctly on few examples at hand. Unfortunately, no esd is given.

dkratzert
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Re: How to know the distance of Cp-M or Arene-M?

Post by dkratzert » 20 Apr 2018, 07:49

Olex2 has advantages there. As long as "MORE -1" is activated, it can calculate the errors correctly itself.

(MORE with negative number writes a .cov file which includes the lists of parameters and the full covariance matrix of the least squares refinement)

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