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Re: Absolute structure

  • To: bm@iucr.org
  • Subject: Re: Absolute structure
  • From: Howard Flack <Howard.Flack@cryst.unige.ch>
  • Date: Wed, 26 Nov 1997 18:40:10 +0100
  After a discussion with G. Bernardinelli and others, two things became
clear:
(I) that for a really meaningful report of absolute configuration (of a
chiral substance) we need a CIF data item for the specific optical
rotation in solution. Again time permitting we will do our best to
produce something clear and complete.
(II) the reporting, using CIF data names, of the hkl region measured and
that used in the refinement is inadequate for our purposes for judging
what was done in absolute structure refinement. I took a very long look
at _reflns_number_total and _reflns_number_Friedel this afternoon and
came up with the following rather long text.

(4) Suggested improvement for core extensions/amendments for:
 
 _reflns_number_total 
 _reflns_number_Friedel
 _reflns_number_gt (for which I have no specific proposal)

Explanation:

  Using the example of a _refln_ list containing four reflections h,k,l;
-h,-k,-l; -h,k,-l; and h,-k,l in space group P2 where:
   h,k,l is equivalent to -h,k,-l, and  
  -h,-k,-l is equivalent to h,-k,l 
  under the operations of the crystal point group.
 
  We always use "Friedel pairs", or "Friedel opposites" to apply only to
the pairs {h,k,l and -h,-k,-l} and {-h,k,-l and h,-k,l} whereas we use
the term "Bijvoet pairs" to apply to {h,k,l and h,-k,l}, {-h,-k,-l and
-h,k,-l}. This leaves a little doubt about what is meant by "Friedel
equivalent" reflections in the proposed definition. But taking it to
mean reflections that are equivalent under the Laue symmetry of the
crystal, the four reflections in my list are Friedel equivalent and the
appropriate value of _reflns_number_Friedel is 4 (four). Likewise 
_reflns_number_total takes a value of 4 for my list. 

  On the other hand I have the impression that it is intended that 
_reflns_number_total applies to "unique" reflections in some way that is
not defined anywhere in the dictionary. For example Acta
Crystallographica C takes the value of _reflns_number_total and
qualifies it by "independent reflections". So I suppose the idea is that
the reflections should have been averaged or grouped into sets of
reflections symmetry equivalent under the crystal point group. In this
way I come to 2 for the desired value of _reflns_number_total and 1 for
_reflns_number_Friedel for my list. If these are not the desired values
then I would appreciate knowing what was intended.

 Further in the circulated definition of _reflns_number_Friedel the
words "although related by symmetry" are most confusing. There are
several symmetries coming into play:
 (1) the crystal point group (crystal class)
 (2) the Laue symmetry (crystal class + a centre)
 (3) the symmetry of the Fourier transform of a real positive-definite
function. I wonder which symmetry is implied here.

So I propose for the _definitions for 

(i)  data_reflns_number_total 
        with the regret that the data name does not clearly indicate
that a crystal-class unique set is intended:

data_reflns_number_total
    _name                      '_reflns_number_total'
    _category                    reflns
    _type                        numb
    _enumeration_range           0:
    _definition
;              '_reflns_number_total' counts the number of sets of
reflections in the _refln_ list where each set contains reflections that
are equivalent under the point-group symmetry of the crystal (crystal
class), the sets being necessarily disjoint.
;
   

(ii) data_reflns_number_Friedel 
        with the regret that the data name does not clearly indicate
that a Laue-symmetry unique set is intended:

data_reflns_number_Friedel
    _name                      '_reflns_number_Friedel'
    _category                    reflns
    _type                        numb
    _enumeration_range           0:
    _definition
;              '_reflns_number_Friedel' counts the number of sets of
reflections in the _refln_ list where each set contains reflections that
are equivalent under the Laue symmetry of the crystal, the sets being
necessarily disjoint.
;

(iii) NB data_reflns_number_gt needs modifying as well.

 The above definitions would be most useful for understanding whether
adequate data had in fact been measured to determine the absolute
structure of a non-centrosymmetric structure. The two values should take
identical values for a centrosymmetric structure.

 In the print version of Acta Crystallographica C the values of 
_reflns_number_total  and _reflns_number_Friedel could be qualified by
"crystal-class independent reflections" and "Laue-symmetry independent
reflections" respectively.  
H>
H>
(5) Proposed new data names _chemical_absolute_configuration and
_chemical_optical_rotation.

data_chemical_absolute_configuration
    _name                      '_chemical_absolute_configuration'
    _category                    chemical
    _type                        char
    loop_ _enumeration
          _enumeration_detail    rm     'absolute configuration
established by the structure determination of a compound containing a
chiral reference molecule of known absolute
configuration.'
                                 ad     'absolute configuration
established by anomalous dispersion effects in diffraction
measurements on the crystal.'
                                 rmad   'absolute configuration
established by the structure determination of a compound containing a
chiral reference molecule of known absolute configuration
and confirmed by anomalous dispersion effects in
diffraction measurements on the crystal.'
                                 .      'inapplicable'
    _definition
;              In 'Enantiomers, Racemates, and Resolutions' by
Jean-Jacques Andre Collet and Samuel H. Wilen: John Wiley & Sons, New
York, it is stated that "the absolute configuration of a chiral
substance is known when an enantiomeric structure can be assigned to an
optically active sample of a given sign." It is thus always recommended
to report the optical activity in solution of the molecule(s) using
_chemical_optical_rotation.

               Sufficient conditions for the assignment of
_chemical_absolute_configuration are as follows in which Set_E is
defined to be the set of non-centrosymmetric crystal classes { 1, 2, 3,
4, 6, 222, 32, 422, 622, 23, 432}, x(u) is the value of the Flack(1983)
parameter as given by  _refine_ls_abs_structure_Flack, NEAR = 1.6 and
FAR = 5.0. 
If the crystal class is NOT in Set_E then
_chemical_absolute_configuration is 'inapplicable' and must take the
value '.' if present. 
For 'rm' to be valid the crystal class must be in Set_E and the source
of the chiral reference substance of known absolute configuration must
be reported.
For 'ad' to be valid the crystal class must be in Set_E and |x/u| < NEAR
and |(1-x)/u| > FAR.
For 'rmad' to be valid the conditions of both 'rm' and 'ad' must be
fulfilled.
;

data_chemical_optical_rotation
    _name                      '_chemical_optical_rotation'
    _category                    chemical
    _type                        char
    _example                   '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)'
    _definition
;              The optical rotation in solution of the compound is
specified in the following format:
               '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' 
               where:
                 TEMP is the temperature of the measurement in degrees
Celsius,
                 WAVE is an indication of the wavelength of the light
used for the measurement,
                 CONC is the concentration of the solution given as the
mass of the substance in g in 100 ml of solution,
                 SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical rotation in degrees
measured in a cell of length l in dm and c is the value of CONC in g,
and

                 SOLV is the chemical formula of the solvent.
;

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