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proposal for valence items

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: proposal for valence items
  • From: "I. David Brown" <idbrown@mcmail.cis.McMaster.CA>
  • Date: Fri, 29 Sep 2000 14:36:54 +0100 (BST)
Dear colleagues,

	I enclose below a number of items I would like to add to the core
CIF dictionary.  They relate to bond valences which are now widely used in
inorganic crystallography to confirm and analyse the results of crystal
structure determinations.  Bond valences are determined from the bond
lengths and have the useful property that their sum around any atom is
equal to the atomic valence (formal charge).  They are increasingly being
listed with the bond lengths in papers.  The first item on this proposed
extension to the core dictionary would permit bonod valences to be added
to the geom_bond list.

	The other two categories list the parameters used to calculate the
bond valences and their literature sources.  These items might also be
reported in a structure determination paper, particularly when there was
some uncertainty about the appropriate parameters to use, but I need them
primarily for a list of bond valence parameters which I propose to post on
the web.  A sample of this list is given in the example under the
valence_param category.  This list will be kept up to date and will make
it easy for software that calculates bond valences to access the latest
values.  It will also provide a CIF standard that can be used for private
files of bond valences.

	I would appreciates any comments.  If none are forthcoming, I will
seek approval of the DMG for this extension, so it is important
that any concerns be voiced as soon as possible.

			Best wishes

				David


*****************************************************
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
*****************************************************


###################################################################3
# Proposed additions to the coreCIF dictionary for items relating
# to bond valences
# Proposed by I.D.Brown
# 2000-09-29
#
#  The first item in this list 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.
#
####################################
#
#   Item for an existing category
#
####################################
#
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
#
###################################
#
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
#
####################################
#
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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