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Draft Phase Identifier Report version 1

Dear colleagues,

     The last discussion of the Crystallographic Phase Identifier
Working Group (#6) produced one response which has been duly
incorporated in the present document.  I have now prepared a
first draft of our report to the Commission on Crystallographic
Nomenclature which I include below.  This draft is intended to
stimulate further discussion so it can be refined.  It includes a
number of editorial comments dealing with matters that need
further discussion.  There are a couple of items in our terms of
reference we have not yet addressed, in particular the
requirement that the crystallographic databases agree with our
recommendations. Can those of you who represent a database please
discuss these recommendations with your colleagues and let the
rest of the Working Group know whether your database would have
any difficulties in implementing the identifier we recommend?  I
will need a positive answer from each of you before we can submit
our report.

     Please circulate your comments to the whole group at
phase-identifiers@iucr.org before 31 January 2004.  If you need
more time, let me know, the deadline is can be changed if
necessary.

                    Best wishes

                         David Brown

***************************************
I.David Brown, Professor Emeritus of Physics
Brockhouse Institute for Materials Research
McMaster University, Hamilton, Ontario
Canada L8S 4M1
Tel: +905 525 9140 ext 24710
Fax: +905 521 2773
email: idbrown@mcmaster.ca
***************************************

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


DRAFT REPORT OF THE WORKING GROUP ON CRYSTAL PHASE IDENTIFIERS
2003-12-23

1. Introduction
---------------
The International Union of Pure and Applied Chemistry (IUPAC) has
been examining standards for the electronic representation of
chemical information, and as part of this effort it has
established a working group to propose an IUPAC Chemical
Identifier (IChI) which would uniquely identify any chemical
compound appearing in an electronic database.  The IChI working
group approached the Commission on Crystallographic Nomenclature
(CCN) of the International Union of Crystallography (IUCr) to
enquire if any conventions existed for a crystallographic phase
identifier that might be incorporated into IChI.  As the only
such convention already approved by the CCN (the Phase Transition
Nomenclature) is not readily adaptable for electronic use, the
CCN established the Working Group on Crystalline Phase
Identifiers to make recommendations that could be of use to the
IChI working group.  This document is the report of this Group. 

The Working Group carried out all its discussions by email,
initially independently of the IChI project, but the resulting
recommendations of the two groups are so similar that
incorporating the crystallographic phase information into IChI
should be trivial.

2. Terms of reference of the Working Group
------------------------------------------
The group will recommend to the IUCr Commission on
Crystallographic Nomenclature:

1. The best method of defining a crystalline phase identifier
that uniquely and unambiguously identifies each crystalline phase
in a way that would allow it to be used to link the same material
appearing in different electronic databases.

2. To recommend the best way in which this identifier can be
implemented, including its incorporation in the CCN recommended
phase transition nomenclature.

Keeping in mind that the  primary purpose of the crystal phase
identifier is to allow the properties of a given material to be
located in different databases, the working group should consult
with appropriate crystallographic databases to ensure that the
proposed identifier will be acceptable.

3. Membership
-------------
The following were appointed members of the Working Group:
     David Brown (chair)
     Sidney Abrahams (chair of CCN ex officio)
     Michael Berndt (Crystal Impact) [deceased]
     John Faber (ICDD)
     Vicky Karen (NIST and ICSD)
     Sam Motherwell (CCDC)
     Jean-Claude Toledano (Chair, CCN working group on Phase
                            Transition Nomenclature)
     Pierre Villars (Pauling File)
     John Westbrook (Protein Databank)
     Brian McMahon (IUCr, consultant)

4. General considerations
-------------------------
Early discussions revealed that many phases have not been
sufficiently well characterized to allow an unambiguous
assignment of an identifier, and in some cases phases have been
incorrectly characterized.  In these situations no identifier can
be expected to meet the requirements of the terms of reference
but an identifier may be able to retrieve a number of possible
matches from which the user could make a final choice.

For well characterized materials the working group examined two
models.  In the first an arbitrary character string is assigned
to each crystallographic phase by a competent authority (similar
to the Chemical Abstracts Registry Number)  In the second a
character string is generated from the known properties of the
compound according to a defined set of rules.

The first choice was rejected early on the grounds that we would
be unlikely to find a competent authority willing to take on the
project.  Such an authority would require external funding, since
it would have to assign identifiers on request in a timely manner
and would have to maintain a public list of the identifiers
already assigned.

The second choice has the advantage that the identifier can be
constructed by anyone with access to the information needed to
characterize the material.  The identifier can be kept to a
manageable size because it only needs to include sufficient
information to distinguish between known phases.  Even if more
information about the phase is available, it is not included in
the identifier if it not needed for characterization.  For
example, OsI3, which is known in only one crystalline form, is
fully characterized by its chemical formula alone and no further
information, chemical or crystallographic, needs be included.

The first component of any phase identifier must characterize the
composition and, where necessary, the isomer.  Only then does it
make sense to identify the crystalline form.  Since IChI is
designed to identify the composition and topology of the
compound, the Working Group's job was to suggest an identifier
that would distinguish between the different crystalline forms of
a given compound.

5. The IChI identifier
----------------------
Before presenting the recommendations of the Working Group, we
give a brief description of the proposed IChI identifier.

The IChI working group is recommending an identifier made up of
several components or layers: 

The first (top) layer, which is always present, gives the
chemical composition.  The lower layers are included only if they
are necessary to distinguish between two compounds with the same
composition. 

The second layer distinguishes between different isomers by
describing the bond topology.  It contains several sublayers or
levels, the first gives the bonding topology ignoring all the
bonds to metals, cations and hydrogen atoms, the second level
adds the bonding to fixed hydrogen atoms, the third adds the
bonding to variable hydrogen atom (to distinguish between
tautomers if this is needed) and the fourth level adds bonds to
metal atoms and cations and is used in the rare cases when a
compound forms different coordination isomers.

The third layer contains information on chiral centers and is
included only when it is necessary to distinguish between
stereoisomers. 

The fourth layer is used to identify isotopically enriched
compounds.  Further layers can be added as needed.  For many
compounds only the first layer is needed and for most of the
others it is only necessary to add the top levels of the second
layer.

6. Recommendations
------------------
A layered structure for the identifier was a feature of the early
discussions of the Working Group and the layers that describe the
chemistry closely match those proposed by the IChI working group.


We recommend that the phase identifier be included as part of the
proposed IChI symbol. 

We recommended that the crystallographic characterization appear
in IChI in three additional layers, in the recommendations below
labelled as layers 5, 6 and 7.

Layer 5. gives the state of matter: gas, liquid, crystal etc.
according to the following enumeration list:
                                                  gas       gas phase
                                                  liq       liquid phase
                                                  sol       solid phase 
of unknown form
                                                  xtl       crystalline 
solid
                                                  qxl       quasi-crystal
                                                  amp       amorphous solid
                                                  lxl       liquid 
crystal or other anomalous
                                                          quasi-liquid phase
[Note in draft: These could be reduced to a single letter code if
desired.]
Only if this flag is set to xtl would layers 6 and 7 be needed.

Layer 6. The space group number. 
This layer contains the space group number as given in
International Tables for Crystallography Vol. A.  It consists of
a number between 1 and 230 that uniquely identifies the space
group type.  The only ambiguity occurs for space groups such as
P41 (76) and P43 (78) that are identical except for their
chirality which is more appropriately identified in the IChI
stereochemistry layer.  Chirality is an important molecular
property but the chirality of a crystal, which is often not
determined, is usually only of interest if the crystal contain a
chiral molecule.  Chiral space groups should be treated as
equivalent.  We recommend that only the lowest number of each
chiral pair of space groups be given, but search algorithms
should equivalence these pairs in case the higher space group
number is inadvertently used.  The equivalent space groups are
76=78, 91=95, 92=96, 144=145, 152=153, 169=170, 171=172, 178=179,
180=181, 212=213.

Problems in assigning the space group can arise in several
situations.  Many inorganic compounds have polymorphs with
similar structures that crystallize with different, but related,
space groups.  In these cases it is easy to assign the wrong
space group, if only a subcell of the true crystallographic unit
cell is reported.  Incommensurate modulated structures, which are
frequently associated with polymorphism, have additional
symmetries that do not appear in the standard table of space
groups.  Sometimes an average space group can be assigned, but
this is not always unique. Quasicrystals cannot be assigned a
space group and are best treated as a different state of matter
(see above).

[Note in draft: A possible solution would be to add the letter m
to the space group number to indicate that the true structure has
an incommensurate modulation.  A letter s might be added to
indicate the presence of an undetermined superstructure] 

Layer 7. Wyckoff Sequence
-------------------------
In the rare event that two phases of the same compound have the
same space group, the Wyckoff sequence can be given.  This is a
list containing the Wyckoff letters associated with the occupied
special positions (sites of high symmetry).  Details of the
special positions and their Wyckoff letters for all 230 space
groups are given in International Tables for Crystallography Vol.
A.  Each letter is accompanied by a number indicating the number
of symmetry-independent atoms occupying sites of that kind (the
default number is 1), e.g, 'a d i6' or 'adi6'.  The enumeration
list contains all the letters of the alphabet plus 'alpha' and
the letters are listed in alphabetic order.  Before determining
the Wyckoff sequence it is essential that the structure be
standardized using the program STRUCTURE TIDY (or other program
using the same algorithm) Details are given in
Parthe, E., Gelato, L.M. (1984). Acta Crystallogr. A40, 169-183.
Parthe, E., Gelato, L.M. (1985). Acta Crystallogr. A41, 142-151.
Gelato, L.M., Parthe, E. (1987). J. Appl. Crystallogr. 20,
139-143.

END OF DRAFT REPORT OF WORKING GROUP
---------------------------------------

SOME FURTHER POINTS THAT NEED DISCUSSION
----------------------------------------
There were two other possible items we considered including in
the identifier:  the Bravais symbol and the reduced cell.  Are
these needed in IChI?

The Bravais symbol is redundant if the space group is given.  If
the space group has not been determined, the Bravais symbol may
be known, though there cannot be many examples of this, and if
the space group cannot be determined, would the Bravais symbol be
reliable?

The reduced cell has proved itself useful in finding the same
phase in different databases, with the composition, if given,
used as a secondary key.  Further, if the reduced cell is known,
it is most likely that the space group is also known.  Are there
any occasions when the reduced cell would be needed to
differentiate two different phases with the same space group and
Wyckoff sequence, or should the reduced cell be used at a higher
level?

The above recommendations, if acceptable, would fulfill one
requirement of our terms of reference, namely to define an
identifier that would distinguish between two different
crystalline phases.  Two others items in our terms of reference
still have to be addressed.

1. Would IChI, extended to cover crystalline phases as described
above, be an acceptable identifier for inclusion in all the
crystallographic databases? 

I would like to hear responses to this question from each of the
database representatives on the Working Group.

2. How can this identifier be implemented, including its
incorporation in the CCN approved Phase Transition Nomenclature?

Details of the implementation, including the format, will have to
be decided by the IChI working group if it is to be part of the
layer structure of IChI.  We should work closely with them.

Details of the approved Phase Transition Nomenclature can be
found on the IUCr web page: Look for Commissions, Commission on
Crystallographic Nomenclature, CNOM on-line information, and
Structural Phase Transition Nomenclature.  The phase transitions
are identified by the two phases that bracket the transition, so
the nomenclature is more properly a nomenclature of the phases
themselves.  The information given in the Phase Transition
Nomenclature includes:

1. the common symbol used to identify this phase (e.g., alpha,
II, etc.),

2. the temperature (and pressure) range in which it is stable,

3. the Hermann-Mauguin symbol and number of the space group (more
than one space group may be given, or the Bravais symbol may be
given if the space group is not known),

4. Z, the number of formula units in the conventional unit cell
(though the formula unit is not defined within the symbol),

5. the ferroic properties and

6. the structure type. 

Any field may be omitted if inapplicable or the value is not
known.  The intent of this symbol is to include the maximum
amount of information about the phase, whereas the philosophy of
IChI is to include only the minimum needed for phase
identification.  The phase transition nomenclature was not
designed for uniqueness nor for electronic coding.  On the other
hand IChI is primarily intended to provide a unique
identification for use in computer-based systems.  The two
symbols therefore are complementary and serve different purposes.
Both include the space group, but otherwise there is little
overlap between them.  The Phase Transition Nomenclature could be
extended by adding the IChI, but it is not clear what advantage
this would provide.  Would it be better to recognize, that since
the two symbols are designed for different purposes, they are
best kept separate?

End of queries for discussion
-----------------------------
End of document

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