Ambiguity in atom_site.disorder_group value -1

Mon Oct 24 12:03:21 BST 2022

On 20/10/2022 00:01, Robert Hanson via coreDMG wrote:
> Maybe more to the point, here. My query is really not about 
> documentation language. What I'm interested in is the way the -1 value 
> should be interpreted. ...
>
> What I would be interested in is some way in the CIF to be able to 
> describe this "localness" of the disorder. That, for example, the 
> results of symop 1 and symop 2 are paired. And, likewise, in this case 
> I presented, symops paired as [1,2], [3,4], [5,6], and [7,8]. Wouldn't 
> this be useful information?
>
> Perhaps something like:
>
> *loop_
> *
> *_local_disorder_id
> *
> *_local_disorder_assembly  # matches atom_site_disorder_assembly
> *
> **
> *_local_disorder_group  # matches atom_site_disorder_group
> *
> *_local_disorder_assembly_symmetry_operation_set #matches list of 
> space_group_symop_id*
> *1 A -1 1,2
> *
> *2 A -1** 3,4
> *
> *3 A -1** 5,6
> *
> *4 A -1** 7,8*
> ...
> Would that be a reasonable feature request?
>
> Bob

I often find it difficult to understand all the ramifications of a 
discussion such as this purely in the abstract, so I looked for a 
real-world example to see how this is currently treated in the 
literature. The example I have found was published in /Acta Cryst. E/: 
https://journals.iucr.org/e/issues/2022/11/00/jy2022/

The ATOM_SITE loop for this structure appears in the CIF as

loop_

_atom_site_type_symbol

_atom_site_label

_atom_site_fract_x

_atom_site_fract_y

_atom_site_fract_z

_atom_site_U_iso_or_equiv

_atom_site_adp_type

_atom_site_calc_flag

_atom_site_occupancy

_atom_site_disorder_assembly

_atom_site_disorder_group

Ni Ni1 0.500000 0.11950(2) 0.250000 0.01509(10) Uani d 1 . .

N N1 0.54965(7) 0.11278(9) 0.10148(12) 0.0185(2) Uani d 1 . .

C C1 0.57231(7) 0.08251(10) 0.01406(14) 0.0165(2) Uani d 1 . .

S S1 0.60344(2) 0.03798(3) -0.11091(4) 0.01977(10) Uani d 1 . .

N N11 0.58540(6) 0.24076(9) 0.38595(12) 0.0181(2) Uani d 1 . .

C C11 0.62454(8) 0.22828(11) 0.53994(15) 0.0204(3) Uani d 1 . .

H H11 0.607248 0.168907 0.584775 0.025 Uiso calc 1 . .

C C12 0.68901(8) 0.29758(12) 0.63729(16) 0.0244(3) Uani d 1 . .

C C13 0.71270(9) 0.38429(13) 0.56974(18) 0.0297(3) Uani d 1 . .

H H13 0.756660 0.433386 0.631780 0.036 Uiso calc 1 . .

C C14 0.67207(10) 0.39913(13) 0.41148(19) 0.0309(3) Uani d 1 . .

H H14 0.687354 0.458893 0.363972 0.037 Uiso calc 1 . .

C C15 0.60876(9) 0.32557(12) 0.32326(16) 0.0240(3) Uani d 1 . .

H H15 0.581066 0.335802 0.214608 0.029 Uiso calc 1 . .

C C16 0.73170(9) 0.27472(15) 0.80794(17) 0.0336(3) Uani d 1 . .

H H16A 0.696992 0.226009 0.835783 0.050 Uiso calc 1 . .

H H16B 0.741856 0.346916 0.864123 0.050 Uiso calc 1 . .

H H16C 0.784063 0.236346 0.835127 0.050 Uiso calc 1 . .

N N21 0.4958(3) 0.5343(3) 0.0380(4) 0.0525(8) Uani d 0.5 A -1

C C21 0.4990(2) 0.5882(3) 0.1369(4) 0.0366(7) Uani d 0.5 A -1

C C22 0.4981(19) 0.6557(4) 0.238(3) 0.059(3) Uani d 0.5 A -1

H H22A 0.511446 0.613590 0.333381 0.089 Uiso calc 0.5 A -1

H H22B 0.443345 0.689575 0.200183 0.089 Uiso calc 0.5 A -1

H H22C 0.538683 0.716083 0.258413 0.089 Uiso calc 0.5 A -1

Figure 5 of the paper shows disordered acetonitrile molecules (for 
example in the middle of the unit cell as viewed), and is nicely 
reproduced by /Jmol/ when all symmetry operations of the space group

_space_group_name_H-M_alt'C 1 2/c 1'

_space_group_name_Hall'-C 2yc'

are applied:

If one looks at the area where the disorder occurs (around the 
acetonitrile molecule) in /Jmol/, showing superimposition of all 
symmetry-generated copies, one gets the following view:

Consider the green and purple pair; they are related through an 
inversion point (which /Jmol/ can render as the little yellow sphere):

Let me call this configuration “nose-to-nose” (as a fanciful description 
of the shape and orientation of the molecules in this view). Likewise 
the orange and turquoise pair are related by inversion (this I’ll call 
“shoulder-to-shoulder”):

while the orange and purple are related by a /c/-glide plane:

Let me call this “nose-to-shoulder”. Now, note that Figure 1 of the 
original publication suppresses some of the disorder, and shows a neater 
arrangement of the acetonitrile molecules:

At first I thought this was a selection of “nose-to-nose” arrangements, 
but along this axis that’s not easy to tell – in projection all the 
possible configurations show a similar shape. However, it demonstrates 
that authors may feel a need to select among the disordered possibilities.

So the questions that come to my mind are:

(1) How did the authors produce their “tidy” Fig. 1? They cite the 
software they have used as Computer programs: /CrysAlis PRO/ (Rigaku OD 
(2021). CrysAlis PRO. Rigaku Oxford Diffraction), /SHELXT/2014/5 
(Sheldrick, G. M. (2015a). /Acta Cryst/. A*71*, 3-8), /SHELXL/2016/6 
(Sheldrick, G. M. (2015b). /Acta Cryst/. C*71*, 3-8), /DIAMOND/ 
(Brandenburg, K. & Putz, H. (1999). /DIAMOND/. Crystal Impact GbR, Bonn, 
Germany) and publCIF (Westrip, S. P. (2010). /J. Appl. Cryst/. *43*, 
920-925). I suspect that the visualization software /DIAMOND/ was what 
they used for the figure.

(2) Is the selected pairing purely a rendering choice? /I.e/. the author 
can perhaps use the visualization software to show any one or more of 
the eight possible locations of the symmetry-transformed atoms. This is 
what /Jmol/ is currently doing, although its right-click menu allows 
only each individual symmetry operation to be rendered, and notpairs or 
other combinations. (It does, though, allow the superposition of *all* 
the symmetry operations.)

I note that in this example, if you consider the specific “pocket” that 
I have singled out, it is populated by the imposition of four of those 
symmetry operations, but not by the other four. (I suppose this is 
implied by the site occupancy factor of 0.5 for these atoms.) So if I 
(as an author) wanted to show all the pockets populated by particular 
orientations of the acetonitrile molecule, I would choose the half of 
the symmetry operations that would combine to provide me with my 
preferred rendering.

If I am not a crystallographically sophisticated user (which I am not), 
I might find this confusing or difficult to show. Could /Jmol/ (without 
additional guidance) offer a choice of renderings which would populate 
the extended structure views with sets of symmetry-generated but not 
overlapping mates? /E.g/. in my example below, I have selected the 
symmetry operations that /Jmol/ labels internally as A (yellow in this 
figure), D (red), B (green) and F (white).

And if I wanted to import this view into, say, /DIAMOND/, then /Jmol/ 
could write the specific choices into a table such as Bob suggests, so 
that /DIAMOND/ (or /Mercury/) would reproduce that view. This is 
certainly a use case for selecting particular disorder configurations, 
although it’s for the benefit of rendering programs rather than a 
physico-chemical description of the crystal structure.

(3) … which leads me to my third question, aimed at the 
crystallographers on the list. Are there refinement strategies (in 
/SHELX/ or other software) that allow you to constrain the local 
symmetries at different locations? /I.e/. in my terminology, if the 
pocket at the centre of the unit cell contains “nose-to-nose” molecules, 
can you constrain the neighbouring pockets to be “shoulder-to-shoulder”? 
Would you even want to be able to do this? Are there any experimental 
features in the diffraction images that would give you some clue as to 
the distribution of those orientations? I would guess that cases like 
this are fairly rare – energetically the different orientations within 
the pocket must be very similar, but perhaps there are weak non-bonding 
interactions that do bias particular combinations. Might every pocket 
contain a “nose-to-shoulder” arrangement?

If these structural arrangements are amenable to discovery (or 
enforcement in refinement), then perhaps Bob’s _local_disorder_...items 
do indeed have a place in the crystal structure description.

Brian

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