STRATEGIES IN STRUCTURE DETERMINATION
FROM POWDER DATA
2- Materials unidentified by
the routine approach with PDF-2
If the search/match failed by using the PDF-2 databank, one should try
more. Other databanks contain crystallography related informations :
(Inorganic Crystal Structure Databank), on CD-ROM, contains nearly about
42000 phases of which the structures were determined from single crystal
or powder diffraction data. The atomic coordinates are generally given
(not for 3000 entries) together with the full reference and some other
details. The 1992 version was quasi-complete (?) up to 1988, however the
CD-ROM contained only 2 entries for 1990, 105 for1989, 924 for1988, 1203
for1987 ..etc. One can observe the presence of multiple entries for one
compound in this bank too. There are also a huge quantity of isotypical
compounds (unavoidable). The user should be very careful and make use of
his common critical sense with any databank, including this one. It is
not exhaustive, unfortunately.
- CSD (Cambridge Structural
Databank) on CD-ROM contains about 160000 entries for small organic molecules
and organometallic compounds. This number increases by 10000 each year
- N.I.S.T. CRYSTAL DATA,
on CD-ROM, contains about 200000 entries corresponding to 60000 single
phases (inorganic/organic). Are gathered a large number of published propositions
of indexation. These could be false or the structure (which is the final
proof that a cell is correct) was not necessarily determined. There are
numeorous multiple entries and isotypical compounds in this bank.
is a compilation of data concerning metallic compounds.
To be able to use these databanks, complementary
of the powder diffraction databank, one information which may suffice is
the sample composition. However the best way is to add the cell knowledge.
methods giving access to the cell are to be considered depending on the
presence or not of large enough single crystals in your preparation.
The PDB (Protein Data Bank of
Brookhaven, 5400 entries) has been excluded from this discussion. Indeed,
you have little chance to succeed in a protein structure determination
from standard powder diffraction data (unless it is a small protein or
you are working with a high resolution diffractometer using synchrotron
radiation, eventually at low temperature). A discussion about the limits
of what you can expect to do from powder data will be given later (chapter
The scenario will continue with the study of five real cases :
One compound identified in the ICDD databank, given with a cell proposition
; absent from ICSD although compounds classified as organometallic like
Ni(CO)4 are included ; found in CSD : Na2(COO)2.
This is a simple case chosen as a school case. The study will be by conventional
[Pd(NH3)4]Cr2O7, a typical
case with heavy atoms for testing the Patterson method (and also, why not,
the direct methods). The study will make use of conventional X-ray data.
This compound was peviously listed in the ICDD databank with a false cell
The various (standard) strategies used in structure determinations from
powder diffraction data will be examined at each step of the whole process
for one or several of the examples above, successively in the next parts
of this tutorial. The corresponding data are made
available (together with other data) in the SDPD-D
(Structure Determination from Powder Diffraction - Database).
t-AlF3, more complex than
the two previous ones because the initial model necessary before to begin
to refine the structure by the Rietveld method was the whole structure.
Indeed, Al3+ and F- are isoelectronic and thus their
X-ray diffusion factors are not very different. This is a typical case
for applying direct methods : eleven independent sites should be found
simultaneously. The study was realized by using conventional X-ray data.
This is a beautiful example of the contribution of the powder diffraction
methodologies to the advancing of Science and basic knowledge. The result
was a crystal structure based on an unknown new way to arrange octahedra
exclusively by corner sharing.
beta-BaAlF5, examined by neutron diffraction, to show how more
difficult is the structure determination from neutron data (remember that
determination is not refinement : for a refinement, at least a large part
of the structure should be known). In the reality, this structure was determined
from X-ray data and the accuracy (on F and Al atomic coordinates) was later
improved by refinement from neutron data.
Cimetidine C10H16N6S, a famous example,
previously known from a single crystal study. This case was examined by
synchrotron radiation in order to estimate the feasibility limits by the
powder methods several years ago (see R.J. Cernik, A.K. Cheetham, C.K.
Prout, D.J. Watkin, A.P. Wilkinson & B.T.M. Willis, J. Appl. Cryst.24
See also the 2 samples of the SDPD
Copyright © 1997- Armel