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Re: proposal for valence items

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: proposal for valence items
  • From: "I. David Brown" <idbrown@mcmail.cis.McMaster.CA>
  • Date: Tue, 28 Nov 2000 19:37:17 GMT
	I have enclosed below the revised version of the changes that are
proposed for the Core dictionary including the valence items I originally
proposed and the new definition proposed by Howard Flack.  I would ask for
approval from the members of the Core Dictionary Maintenance Group (DMG).  
According to my records these include Brown, McMahon, Hall, Spek and
Johnson (replacing Edgington).  Comments from anyone else are also
welcome.  Once the DMG has given approval this will be moved to Comcifs
for approval and then be incorporated into core_CIF.

				David

more below, keep scrolling
*****************************************************
Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research, 
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************

#############################################################
# Proposed additions to the coreCIF dictionary for items relating 
# to bond valences and other matters
#
# 2000-11-28
# Version 0.02
# When added to Core version 2.1 it will creat core_CIF version 2.2
#
#  The first item in this list is a change in the definition related
#  to absolute configuration.
#
#  The next item allows for bond valences to be
#  added to bond length tables.
#
#  The valence_param category contains items that would appear as 
#  a table of bond valence parameters.
#  This could be made available (e.g. on the web) in a form in 
#  which it can be easily edited and read into any program that 
#  wishes to calculate bond valences from bond lengths.
#  
#  The valence_ref category lists the papers from which the bond 
#  valence parameters have been taken.
#
###################################
#
#   Change in the definition of an existing item
#   Proposed by Howard Flack
#
###################################
#
data_chemical_absolute_configuration
#
# Replace the existing rather convoluted definition with the following
#
    _definition
;              Necessary conditions for the assignment of
               _chemical_absolute_configuration are given by H. D. Flack and
               G. Bernardinelli in Acta. Cryst. (1999). A55, 908-915 and
               J. Appl. Cryst. (2000). 33, 1143-1148.
;
#
####################################
#
#   Item for an existing category
#   Proposed by David Brown
#
####################################
#
data_geom_bond_valence
  _name         '_geom_bond_valence'
  _definition
;         The bond valence calculated from  _geom_bond_distance
;
  _category      geom_bond
  _list          yes
  _type          numb
#
###################################
#
#   VALENCE_PARAM
#   A new category proposed by David Brown
#
###################################
#
data_valence_param
  _name           'valence_param'
  _definition
;   Items in this category define the parameters used for calculating bond
valences from bond lengths.  In addition to the parameters, a pointer is given
to the reference (in valence_ref) where the parameters have been published
;
  _category       category_overview
  _type           null
  loop_ _example
        _example_detail
;  loop_ _valence_param_atom_1
         _valence_param_atom_1_valence
         _valence_param_atom_2
         _valence_param_atom_2_valence
         _valence param_Ro
         _valence_param_B
         _valence_param_ref_id
         _valence_param_details
Cu 2 O -2 1.679 0.37 a .
Cu 2 O -2 1.649 0.37 j .
Cu 2 N -3 1.64  0.37 m '2-coordinate N'
Cu 2 N -3 1.76  0.37 m '3-coordinate N'
    loop_ _valence_ref_reference_id
          _valence_ref_reference 
a  'Brown and Altermatt, 1985, Acta Cryst. B41 244-247'
j  'Liu and Thorp, 1993, Inorg. Chem. 32, 4102-4205'
m  'See, Krause and Strub, 1998, Inorg. Chem. 37, 5369-5375'
;         
;An example of a bond valence parameter list with accompanying references.
;
#
#
data_valence_param_atom_1
  _name           '_valence_param_atom_1'
  _definition
;   The element symbol of the first atom forming the bond whose
bond valence parameters are given in this category.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           char
#
#
data__valence_param_atom_1_valence
  _name           '_valence_param_atom_1_valence'
  _definition
;   The valence (formal charge) of the first atom whose bond
valence parameters are given in this category.
;
  _category       valence_param 
  _list           yes
  _list_reference '_valence_param_id'
  _type           numb
#
#
data_valence_param_atom_2
  _name           '_valence_param_atom_2'
  _definition
;   The element symbol of the second atom forming the bond whose
bond valence parameters are given in this category.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           char
#
#
data_valence_param_atom_2_valence
  _name           '_valence_param_atom_2_valence'
  _definition
;   The valence (formal charge) of the second atom whose bond
valence parameters are given in this category.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           numb
#
#
data_valence_param_B
  _name           '_valence_param_B'
  _definition
;         The bond valence parameter B used in the expression

          s = exp((Ro - R)/B)

where s is the valence of a bond of length R.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           numb
  _units          A
  _units_detail   Angstrom
#
# 
data_valence_param_details
  _name           '_valence_param_details'
  _definition
;  Details or comments on the bond valence parameters.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           char
#
#
data_valence_param_id
  _name           '_valence_param_id'
  _definition
;  An identifier for the valence parameters of a bond between the given atoms.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           char
#
#
data_valence_param_ref_id
  _name           '_valence_param_ref_id'
  _definition
;  An identifier which links to the reference to the source from which the
bond valence parameters are taken.  A child of _valence_ref_id which it must
match.
;
  _category        valence_param
  _list            yes
  _list_reference  '_valence_param_id'
  _type            char
#
#
data_valence_param_Ro
  _name           '_valence_param_Ro'
  _definition
;         The bond valence parameter Ro used in the expression

          s = exp((Ro - R)/B)

where s is the valence of a bond of length R.
;
  _category       valence_param
  _list           yes
  _list_reference '_valence_param_id'
  _type           numb
  _units          A
  _units_detail   Angstrom
#
####################################
#
#    VALENCE_REF
#    A new category proposed by David Brown
#
####################################
#
data__valence_ref
  _name           'valence_ref'
  _definition
;   Items in this category list the references from which the bond valence
parameters have been taken.
;
  _category       category_overview
  _type           null
#
#
data_valence_ref_id
  _name           '_valence_ref_id'
  _definition
;  An identifier for items in this category.  Parent of _valence_param_ref_id
which must have the same value.
;
  _category       valence_ref
  _list           yes
  _list_reference '_valence_ref_id'
  _type           char
#
#
data_valence_ref_reference
  _name           '_valence_ref_reference'
  _definition
;  Literature reference from which the valence parameters identified by
_valence_param_id were taken.
;
  _category       valence_ref
  _list           yes
  _list_reference '_valence_ref_id'
  _type           char

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