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*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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