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Re: Absolute structure
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Re: Absolute structure
- From: Howard Flack <Howard.Flack@cryst.unige.ch>
- Date: Fri, 14 Aug 1998 16:09:07 +0100 (BST)
This is a multi-part message in MIME format. --Boundary_(ID_QJJktNbLOkKnR4HW4vlt9g) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit I forgot to attach the file! -- 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 --Boundary_(ID_QJJktNbLOkKnR4HW4vlt9g) Content-type: text/plain; name=asacs.cifdefn.txt; charset=us-ascii Content-disposition: inline; filename=asacs.cifdefn.txt Content-transfer-encoding: 7bit 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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