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Re: Discussion Paper #4

  • To: Chemical information in core CIF <corecifchem@iucr.org>
  • Subject: Re: Discussion Paper #4
  • From: Greg P Shields <shields@ccdc.cam.ac.uk>
  • Date: Tue, 23 Mar 2004 08:45:14 +0000
  • Organization: CCDC
  • References: <40479052.2050408@mcmaster.ca>
Dear David,

Sorry to bring up the issue of disorder again, but I have been thinking 
about the latest proposals, in particular in how they relate to more 
complex examples of disordered molecules. Whilst I think I can 
understand how  they would be applied to relatively simple cases of 
disorder, I am not sure how this would be extended to larger molecules 
with a number of independently disordered groups. In such cases, there 
could be a large number of possible combinations of the submappings for 
each of the disordered groups in one molecule, and hence a large total 
number of mappings for the whole molecule. I am concerned that the 
description could become unwieldy in such cases, and perhaps we may need 
to consider only storing the mapping of the atoms common to all 
configurations once, along with one configuration of each of the 
disordered groups, using sub-mappings to describe the other 
configurations of the disordered groups.

I expect you have already considered these problems, and I think it 
would be useful to know how you were considering dealing with more 
complex cases in these proposals. I have attached a portion of a CIF 
describing a molecule with twofold disorder in two propylene bridges 
(with occupancies 0.62/0.38 and 0.55/0.45 respectively) as an example 
slightly more complex cases (this is taken from a CIF deposited at the 
CCDC - Journal : Dalton Trans. (0222), P: 2872, Y: 2003;
Authors: L.Salmon,P.Thuery,E.Riviere,J.-J.Girerd,M.Ephritikhine).
I would be interested to hear how this would be described in the 
proposed framework.

> 
> IDB response:
> In the first round I wanted to make sure that we agreed on
> principles before tackling problems such as disorder, but I am
> glad that Greg raised this point because this is the right time
> to consider it.  The answer is surprisingly simple: A disordered
> crystal contains two images of the molecule.  They may be
> geometrically identical if the molecules are disordered around
> say a two-fold axis, or they may represent different conformers
> if say a methyl group is disordered over two geometrically
> different sites.  Although the two images will normally have the
> same graph, we can treat them as two different components each
> having an occupation number less than 1.0; one of the components
> maps onto one set of disordered atoms and the other maps onto the
> second.  Many of the atoms in the two graphs will map onto the
> same atom in the crystal, but this is not a problem provided the
> sum of their occupation numbers does not exceed 1.0.  If the
> occupation numbers of the two independent molecules in the
> formula unit exceeds 1.0 they have to map into different parts of
> the unit cell (the case of Z' > 1).  This approach also works for
> occupational disorder where the components contain different
> elements that map onto the same site in the crystal. The two
> partially-occupied component graphs in the formula unit may or
> may not be isomorphous.  The implications of this are worked out
> in the proposal below.
> 

Best regards,
-- 
Greg Shields
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ
Greg.Shields@ccdc.cam.ac.uk  http://www.ccdc.cam.ac.uk/

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
U U 0.107185(18) 0.731780(15) 0.281688(12) 0.02818(7) Uani 1 1 d . . .
Zn1 Zn -0.01872(5) 0.68437(4) 0.47732(4) 0.02947(14) Uani 1 1 d . . .
Zn2 Zn 0.18981(6) 0.80843(5) 0.08058(4) 0.03646(16) Uani 1 1 d . . .
O1 O -0.0375(3) 0.6345(3) 0.1954(2) 0.0337(9) Uani 1 1 d . . .
O2 O -0.0400(3) 0.6411(3) 0.3532(2) 0.0295(8) Uani 1 1 d . . .
O3 O 0.1295(3) 0.7382(3) 0.4309(2) 0.0316(8) Uani 1 1 d . . .
O4 O 0.2776(3) 0.8221(3) 0.3406(2) 0.0332(8) Uani 1 1 d . . .
O5 O -0.0029(3) 0.8575(3) 0.3110(2) 0.0353(9) Uani 1 1 d . . .
O6 O 0.1152(3) 0.8545(3) 0.1832(2) 0.0326(8) Uani 1 1 d . . .
O7 O 0.2171(3) 0.7097(3) 0.1618(2) 0.0346(9) Uani 1 1 d . . .
O8 O 0.2036(3) 0.5954(3) 0.2791(2) 0.0345(9) Uani 1 1 d . . .
N1 N -0.1386(4) 0.5628(4) 0.4923(3) 0.0398(12) Uani 1 1 d D . .
N2 N 0.0670(4) 0.6994(3) 0.5935(3) 0.0323(10) Uani 1 1 d . . .
N3 N 0.1976(5) 0.9516(4) 0.0464(3) 0.0473(13) Uani 1 1 d . . .
N4 N 0.3284(5) 0.7671(4) 0.0206(3) 0.0555(15) Uani 1 1 d D . .
C1 C -0.1201(5) 0.5720(4) 0.2235(4) 0.0328(12) Uani 1 1 d . . .
C2 C -0.1217(4) 0.5756(4) 0.3095(3) 0.0273(11) Uani 1 1 d . . .
C3 C -0.2045(5) 0.5123(4) 0.3465(4) 0.0328(12) Uani 1 1 d . . .
C4 C -0.2846(5) 0.4442(4) 0.2933(4) 0.0372(13) Uani 1 1 d . . .
H4 H -0.3399 0.4014 0.3158 0.045 Uiso 1 1 calc R . .
C5 C -0.2819(5) 0.4402(4) 0.2095(4) 0.0383(14) Uani 1 1 d . . .
H5 H -0.3348 0.3943 0.1757 0.046 Uiso 1 1 calc R . .
C6 C -0.2005(5) 0.5044(4) 0.1735(4) 0.0357(13) Uani 1 1 d . . .
H6 H -0.2004 0.5017 0.1164 0.043 Uiso 1 1 calc R . .
C7 C -0.2063(5) 0.5090(4) 0.4346(4) 0.0351(13) Uani 1 1 d . . .
H7 H -0.2628 0.4626 0.4519 0.042 Uiso 1 1 calc R . .
C8A C -0.1456(8) 0.5264(7) 0.5756(4) 0.036(2) Uiso 0.623(12) 1 d PDU . .
C9A C -0.1233(7) 0.6179(6) 0.6395(5) 0.038(2) Uiso 0.623(12) 1 d PDU . .
C8B C -0.1732(13) 0.5695(12) 0.5806(6) 0.033(3) Uiso 0.377(12) 1 d PDU . .
C9B C -0.0695(12) 0.5686(8) 0.6407(9) 0.035(4) Uiso 0.377(12) 1 d PDU . .
C10 C 0.0022(5) 0.6674(5) 0.6635(4) 0.0421(14) Uani 1 1 d D . .
C11 C 0.1720(5) 0.7378(4) 0.6109(3) 0.0328(12) Uani 1 1 d . . .
H11 H 0.1990 0.7408 0.6660 0.039 Uiso 1 1 calc R . .
C12 C 0.2549(5) 0.7777(4) 0.5557(3) 0.0305(12) Uani 1 1 d . . .
C13 C 0.2297(4) 0.7781(4) 0.4704(3) 0.0287(11) Uani 1 1 d . . .
C14 C 0.3117(5) 0.8224(4) 0.4196(3) 0.0307(12) Uani 1 1 d . . .
C15 C 0.4193(5) 0.8640(4) 0.4568(4) 0.0355(13) Uani 1 1 d . . .
H15 H 0.4743 0.8930 0.4246 0.043 Uiso 1 1 calc R . .
C16 C 0.4468(5) 0.8634(4) 0.5411(4) 0.0388(14) Uani 1 1 d . . .
H16 H 0.5197 0.8910 0.5643 0.047 Uiso 1 1 calc R . .
C17 C 0.3668(5) 0.8222(4) 0.5899(4) 0.0358(13) Uani 1 1 d . . .
H17 H 0.3856 0.8231 0.6462 0.043 Uiso 1 1 calc R . .
C18 C -0.0108(5) 0.9301(4) 0.2633(3) 0.0343(13) Uani 1 1 d . . .
C19 C 0.0541(5) 0.9295(4) 0.1937(3) 0.0349(13) Uani 1 1 d . . .
C20 C 0.0568(6) 1.0052(4) 0.1406(4) 0.0443(15) Uani 1 1 d . . .
C21 C -0.0143(7) 1.0798(5) 0.1573(4) 0.0558(19) Uani 1 1 d . . .
H21 H -0.0154 1.1303 0.1229 0.067 Uiso 1 1 calc R . .
C22 C -0.0807(6) 1.0792(5) 0.2225(4) 0.0520(17) Uani 1 1 d . . .
H22 H -0.1265 1.1290 0.2319 0.062 Uiso 1 1 calc R . .
C23 C -0.0807(5) 1.0038(4) 0.2759(4) 0.0419(14) Uani 1 1 d . . .
H23 H -0.1276 1.0033 0.3196 0.050 Uiso 1 1 calc R . .
C24 C 0.1314(7) 1.0130(5) 0.0741(4) 0.0528(18) Uani 1 1 d . . .
H24 H 0.1319 1.0704 0.0475 0.063 Uiso 1 1 calc R . .
C25 C 0.2742(7) 0.9827(5) -0.0200(4) 0.068(2) Uani 1 1 d D . .
C26A C 0.3809(10) 0.9337(8) -0.0250(9) 0.062(4) Uiso 0.554(13) 1 d PDU . .
C27A C 0.3505(14) 0.8231(8) -0.0538(7) 0.059(3) Uiso 0.554(13) 1 d PDU . .
C26B C 0.3086(13) 0.8901(9) -0.0703(9) 0.055(4) Uiso 0.446(13) 1 d PDU . .
C27B C 0.3959(12) 0.8314(11) -0.0330(10) 0.059(4) Uiso 0.446(13) 1 d PDU . .
C28 C 0.3810(6) 0.6950(5) 0.0356(4) 0.0490(17) Uani 1 1 d . . .
H28 H 0.4394 0.6839 0.0015 0.059 Uiso 1 1 calc R . .
C29 C 0.3633(5) 0.6282(5) 0.0976(4) 0.0437(15) Uani 1 1 d . . .
C30 C 0.2841(5) 0.6394(4) 0.1587(3) 0.0339(13) Uani 1 1 d . . .
C31 C 0.2770(5) 0.5765(4) 0.2231(4) 0.0354(13) Uani 1 1 d . . .
C32 C 0.3468(5) 0.5018(5) 0.2253(4) 0.0427(15) Uani 1 1 d . . .
H32 H 0.3418 0.4599 0.2670 0.051 Uiso 1 1 calc R . .
C33 C 0.4248(5) 0.4897(5) 0.1645(4) 0.0473(16) Uani 1 1 d . . .
H33 H 0.4708 0.4396 0.1660 0.057 Uiso 1 1 calc R . .
C34 C 0.4332(5) 0.5517(5) 0.1031(4) 0.0501(18) Uani 1 1 d . . .
H34 H 0.4861 0.5434 0.0640 0.060 Uiso 1 1 calc R . .
N5 N -0.1126(4) 0.8011(3) 0.4846(3) 0.0310(10) Uani 1 1 d . . .
C35 C -0.2041(5) 0.7977(4) 0.4297(4) 0.0381(14) Uani 1 1 d . . .
H35 H -0.2254 0.7404 0.3930 0.046 Uiso 1 1 calc R . .
C36 C -0.2666(5) 0.8745(4) 0.4257(4) 0.0389(14) Uani 1 1 d . . .
H36 H -0.3289 0.8695 0.3869 0.047 Uiso 1 1 calc R . .
C37 C -0.2360(5) 0.9605(4) 0.4807(4) 0.0365(13) Uani 1 1 d . . .
H37 H -0.2782 1.0133 0.4800 0.044 Uiso 1 1 calc R . .
C38 C -0.1414(5) 0.9655(4) 0.5363(4) 0.0376(13) Uani 1 1 d . . .
H38 H -0.1176 1.0224 0.5730 0.045 Uiso 1 1 calc R . .
C39 C -0.0834(5) 0.8850(4) 0.5362(4) 0.0391(14) Uani 1 1 d . . .
H39 H -0.0203 0.8886 0.5741 0.047 Uiso 1 1 calc R . .
N6 N 0.0442(4) 0.7280(3) 0.0131(3) 0.0351(11) Uani 1 1 d . . .
C40 C -0.0611(5) 0.7419(4) 0.0346(4) 0.0385(14) Uani 1 1 d . . .
H40 H -0.0678 0.7946 0.0740 0.046 Uiso 1 1 calc R . .
C41 C -0.1589(5) 0.6817(5) 0.0009(4) 0.0446(15) Uani 1 1 d . . .
H41 H -0.2305 0.6935 0.0170 0.053 Uiso 1 1 calc R . .
C42 C -0.1495(5) 0.6033(5) -0.0574(4) 0.0444(15) Uani 1 1 d . . .
H42 H -0.2149 0.5616 -0.0811 0.053 Uiso 1 1 calc R . .
C43 C -0.0427(6) 0.5874(5) -0.0801(4) 0.0550(18) Uani 1 1 d . . .
H43 H -0.0342 0.5343 -0.1185 0.066 Uiso 1 1 calc R . .
C44 C 0.0521(6) 0.6526(5) -0.0442(4) 0.0469(16) Uani 1 1 d . . .
H44 H 0.1243 0.6434 -0.0607 0.056 Uiso 1 1 calc R . .

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