[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

# 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. ;

**[Send comment to list secretary]****[Reply to list (subscribers only)]**- Prev by Date:
**Re: Absolute structure** - Next by Date:
**Re: Enumeration ranges** - Prev by thread:
**Re: Absolute structure** - Next by thread:
**Re: Absolute structure** - Index(es):