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Absolute structure

  • To: bm@iucr.org
  • Subject: Absolute structure
  • From: Howard Flack <Howard.Flack@cryst.unige.ch>
  • Date: Tue, 18 Nov 1997 11:40:32 +0100
  • Organization: University of Geneva
  • References: <199711171522.PAA07676@agate.iucr.ac.uk>
(1) For "data_refine_ls_abs_structure_Flack" I suggest the amended form
given below. The justification is as follows, u being the standard
uncertainty of x.

For centrosymmetric structures the value of the parameter is undefined.
The producer of a CIF has two options: (i) leave out the data name and
corresponding value all together or (ii) include the data name with a
value of 'inapplicable' represented by '.' .

For noncentrosymmetric structures, the physical range of the parameter
is 0 =< x =< 1 but statistical fluctuations in the observations lead to
statistical fluctuations in the value of x obtained by least-squares
refinement which may thus lie outside the physical range within a few
standard uncertainties. In fact as the vast majority of samples are
indeed single crystals the most common values of x are 'close' to either
0 or 1, the boundaries of the physical range.

Within the current CIF dictionary definitions, it is not possible to
express the above interval of x correctly in _enumeration range. I have
taken the liberty of breaking the rules in order to express my intent.


data_refine_ls_abs_structure_Flack
    _name                      '_refine_ls_abs_structure_Flack'
    _category                    refine
    _type                        numb
    _type_conditions             esd
    _enumeration_range           -3.0*u:1.0+3.0*u
    _definition
;              The measure of absolute structure (enantiomorph or polarity) as
               defined by Flack.
 
               For centrosymmetric structures the only permitted value, if the 
               data name is present, is 'inapplicable' represented by '.' .

               For non-centrosymmetric structures the value must lie in the
               99.97% Gaussian confidence interval  -3u =< x =< 1 + 3u and a
               standard uncertainty (e.s.d.) u must be supplied.

               Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
;

(2) In this example, I have made two suggested changes:

(2a) The line
          _refine_ls_abs_structure_Flack     0
      has been removed. According to the comment in 
_refine_ls_abs_structure_details an absolute configuration has been
assigned, not obtained using x by least-squares refinement. There is
thus no standard uncertainty on x and no information available that the
assigned value is confirmed by the diffraction measurements. In fact x
has not been used at all. In such cases the use of the 
_refine_ls_abs_structure_Flack data name seems completely inappropriate.

(2b) 
    _refine_ls_abs_structure_details
    ;      The absolute configuration was assigned to agree
           with the known chirality at C3 arising from its
           precursor l-leucine.
    ;
See the modified version below. Glossing over the inclusion of the
letters 'ls' - 'least squares' in the data name, despite the fact that
in this case nothing concerning the absolute structure has been obtained
from the diffraction data by least squares, the wording has been changed
to remove 'chirality'. In the physics and chemical literature, (Lord
Kelvin; Whyte; Cahn, Ingold & Prelog, Prelog), the notion of a chiral
object is always clearly defined and in essence the same: [[(VP76) "An
object is chiral if it cannot be brought into congruence with its mirror
image by translation and rotation.  Such objects are devoid of symmetry
elements which include reflection: mirror planes, inversion centres, or
improper rotational axes." ]]. On the other hand the above authors do
not offer an unequivocal definition of chirality and its exact or
implied meaning is obscure. Glazer and Stadnicka even go as far to use
chirality to mean optical activity for which the symmetry restrictions
are different from those of a chiral object. So I prefer not to use
chirality. On the other hand the term 'absolute configuration', although
horrid (like absolute structure), is clear in the chemical literature
although not always applied rigorously in publications of the IUCr.


############
## REFINE ##
############

data_refine_[]
    _name                      '_refine_[]'
    _category                    category_overview
    _type                        null
    loop_ _example
          _example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
    _refine_special_details            sfls:_F_calc_weight_full_matrix

    _refine_ls_structure_factor_coef   F
    _refine_ls_matrix_type             full
    _refine_ls_weighting_scheme        calc
    _refine_ls_weighting_details      'w=1/(\s^2^(F)+0.0004F^2^)'
    _refine_ls_hydrogen_treatment      refxyz
    _refine_ls_extinction_method       Zachariasen
    _refine_ls_extinction_coef         3514(42)
    _refine_ls_extinction_expression
    ;  Larson, A. C. (1970). "Crystallographic Computing",
       edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
    ;
    _refine_ls_abs_structure_details
    ;      The absolute configuration was assigned to agree with that of 
           its precursor l-leucine at the chiral centre C3.
    ;
    _refine_ls_number_reflns           1408
    _refine_ls_number_parameters       272
    _refine_ls_number_restraints       0
    _refine_ls_number_constraints      0
    _refine_ls_R_factor_all            .038
    _refine_ls_R_factor_obs            .034
    _refine_ls_wR_factor_all           .044
    _refine_ls_wR_factor_obs           .042
    _refine_ls_goodness_of_fit_all    1.462
    _refine_ls_goodness_of_fit_obs    1.515
    _refine_ls_shift/esd_max           .535
    _refine_ls_shift/esd_mean          .044
    _refine_diff_density_min          -.108
    _refine_diff_density_max           .131

(3) I'm beginning to wonder why the chemical crystallographers and the
chemical data base people have not started to cry out for an
'absolute_configuration_determined' CIF data name.

-- 
Howard Flack        http://www.unige.ch/crystal/ahdf/Howard.Flack.html
Laboratoire de Cristallographie               Phone:(+41 22) 702 62 49
24 quai Ernest-Ansermet             mailto:Howard.Flack@cryst.unige.ch
CH-1211 Geneva 4, Switzerland                   Fax:(+41 22) 781 21 92

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