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Re: Absolute structure



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-- 
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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Determining and reporting Absolute Structure and Absolute Configuration

by H. D. Flack and G. Bernardinelli


  PROPOSED addenda and modifications to the CIF (core) data names and definitions [asacs.cifdefn.txt]. This document will not be deposited as supplementary material as we do not want copies of a PROPOSAL to the cif core to be available as an archive. Users should refer only to the official versions of the CIF core dictionary. 


Version 14th August 1998

Proposed changes to the CIF core for Absolute Structure and Absolute Configuration
==================================================================================



(1) Modification to _refine_ls_abs_structure_Flack
    ----------------------------------------------

data_refine_ls_abs_structure_Flack
    _name                      '_refine_ls_abs_structure_Flack'
    _category                    refine
    _type                        numb
    _type_conditions             esd
    _enumeration_range           0:1.0
    _definition
;              The measure of absolute structure 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. The 
               _enumeration_range of 0.0:1.0 defined above is correctly 
               interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u) 

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


(2) Modification to the REFINE example
    ----------------------------------



############
## 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) Proposed new data name _chemical_absolute_configuration
    -------------------------------------------------------
   

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.
;
                                 syn   
;                                        absolute configuration has not been
                                         established by anomalous dispersion 
                                         effects in diffraction measurements on 
                                         the crystal. The enantiomer has been 
                                         assigned by reference to an unchanging 
                                         chiral centre in the synthetic procedure.
;
                                 unk   
;                                        absolute configuration is unknown
                                         there being no firm chemical evidence
                                         for its assignment to hand and it
                                         having not been established by
                                         anomalous dispersion effects in
                                         diffraction measurements on the
                                         crystal. An arbitrary choice of
                                         enantiomer has been made.
;
                                 .      'inapplicable'
    _definition
;              Necessary 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. The optical activity in solution
               or liquid state must be non-zero.

               For 'ad' to be valid the crystal class must be in Set_E and
               |x/u| < NEAR and |(1-x)/u| > FAR. The optical activity in solution
               or liquid state must be non-zero.

               For 'rmad' to be valid the conditions of both 'rm' and 'ad' must
               be fulfilled.  The optical activity in solution or liquid state 
               must be non-zero.

               For 'syn' to be valid the crystal class must be in Set_E and the
               chiral centre used to assign the enantiomer must be reported.
               The optical activity in solution or liquid state must be non-zero.

               For 'unk' to be valid the crystal class must be in Set_E. The 
               optical activity in solution or liquid state must be non-zero.

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



(4) Proposed new data name _chemical_optical_rotation
    -------------------------------------------------

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.
;


(5) Modification to _reflns_number_total
    -----------------------------------



data_reflns_number_total
    _name                        '_reflns_number_total'
    _category                    reflns
    _type                        numb
    _enumeration_range           0:
    _definition
;              The total number of reflections in the _refln_ list (not the
                _diffrn_refln_ list). It may include Friedel equivalent
               reflections (i.e. those which are symmetry equivalent under the
               Laue symmetry but inequivalent under the crystal class) 
               according to the nature of the structure and the procedures 
               used. The item _reflns_special_details  describes the reflection
               data.
;


(6) Modification to _reflns_number_gt
    ---------------------------------


data_reflns_number_gt
    _name           '_reflns_number_gt'
    _category       reflns
    _type           numb
    _enumeration_range      0:
    _definition     
;              The number of reflections in the _refln_ list (not the
               _diffrn_refln_ list) that are significantly intense,
               satisfying the criterion specified by
               _reflns_threshold_expression. It may include Friedel
               equivalent reflections (i.e. those which are symmetry equivalent
               under the Laue symmetry but inequivalent under the crystal class)
               according to the nature of the structure and the procedures used.
               The item _reflns_special_details describes the reflection data.
;
 


(7) Proposed new data name _reflns_number_Friedel
    ---------------------------------------------
    
    Do not implement the suggested new data name _reflns_number_Friedel



(8) Proposed new data name _reflns_Friedel_coverage
    -----------------------------------------------


data_reflns_Friedel_coverage
    _name                      '_reflns_Friedel_coverage'
    _category                    reflns
    _type                        numb
    _enumeration_range           0.0:1.0
    _definition
;              The proportion of Friedel related reflections present in 
               the number of the "independent reflections" specified by 
               the item _reflns_number_total

               This proportion is calculated as the ratio:

                 [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) 

               where, working from the _diffrn_refln_ list

               N(Crystal class) is the number of reflections obtained on 
                  averaging under the symmetry of the crystal class 
               N(Laue symmetry) is the number of reflections obtained on 
                  averaging under the Laue symmetry.

               Examples:
                 (a) For centrosymmetric structures its value is
                     necessarily equal to 0.0 as the crystal class 
                     is identical to the Laue symmetry.
                 (b) For whole-sphere data for a crystal in the space
                     group P1, _reflns_Friedel_coverage is equal to 1.0, 
                     as no reflection h k l is equivalent to -h -k -l 
                     in the crystal class and all Friedel pairs
                     {h k l; -h -k -l} have been measured.
                 (c) For whole-sphere data in space group Pmm2, the value 
                     will be < 1.0 because although reflections h k l and 
                     -h -k -l are not equivalent when h k l indices are
                     non-zero, they are when l=0.
                 (d) For a crystal in the group Pmm2 measurements of the 
                     two inequivalent octants h >= 0, k >=0, l lead to the 
                     same value as in (c), whereas measurements of the 
                     two equivalent octants h >= 0, k, l >= 0 will lead to 
                     a zero value for _reflns_Friedel_coverage.
;


--Boundary_(ID_QJJktNbLOkKnR4HW4vlt9g)--


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