Structures of the Transition Metal Halides and Oxides

The Goal

1). To generate web pages to display either Brookhaven PDB or MDL MOL files containing the crystallographic information of some transition metal binary salts.

2). Use readily available (free if possible) software.

The Mechanism

1). Look up STRUCTURE REPORTS or other suitable reference for atomic coordinates or special positions of the atoms, space group and unit cell dimensions.

2). Create SHELX type data file, e.g.
for BiI₃ see Structure Reports, 2, 23-26.

TITL   BiI3
CELL    0.71073    7.516     7.516    20.718    90.00     90.00    120.00          
ZERR      2    0.0010    0.0010    0.0010    0.0100    0.0100    0.0100
LATT   -1
SYMM   -y,x-y,z 
SYMM   -x+y,-x,z 
SYMM  -x,-y,-z 
SYMM  y,-x+y,-z 
SYMM  x-y,x,-z 
SYMM  x+2/3,y+1/3,z+1/3 
SYMM  -y+2/3,x-y+1/3,z+1/3 
SYMM  -x+y+2/3,-x+1/3,z+1/3 
SYMM  -x+2/3,-y+1/3,-z+1/3 
SYMM  y+2/3,-x+y+1/3,-z+1/3 
SYMM  x-y+2/3,x+1/3,-z+1/3 
SYMM  x+1/3,y+2/3,z+2/3 
SYMM  -y+1/3,x-y+2/3,z+2/3 
SYMM  -x+y+1/3,-x+2/3,z+2/3 
SYMM  -x+1/3,-y+2/3,-z+2/3 
SYMM  y+1/3,-x+y+2/3,-z+2/3 
SYMM  x-y+1/3,x+2/3,-z+2/3 
SFAC   Bi I
UNIT      6  18
FVAR   1.0
Bi1      1   0.00000   0.00000   0.16660    11.00000     0.05000
I1       2   0.34150   0.33950   0.08050    11.00000     0.05000
HKLF     4
END

The Space Group is R-3 which defines the necessary SYMM operations above. These can be obtained from the on-line space group tables at http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list.

3). Load the file into ORTEP3 for Windows.
http://www.chem.gla.ac.uk/~louis/ortep3

4). Use the "Unit Cell Contents" menu option under "Contents" to grow the cell in the direction you want and as big as you want.

5). Export the file as a SHELX file. Rename from SHELX001.INS to BiI3.she

6). Convert the file to PDB or MOL using BABEL for Windows and BABEL 1.6.
http://www.ccl.net/cca/software/SOURCES/C/babel/index.shtml
and http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/tagon.htm

7). Check you typed the coordinates in properly or otherwise admire your handiwork with WebLabViewer.
http://www.msi.com/

8). Rotate until you find layer structures.

9). Use a text editor to rename the anions according to layer.

10). Create CHIME scripts to highlight atoms and layers.
To LOAD a file and set spacefill sizes to represent ionic radii.

<embed src="nacl.pdb" width="350" height="350"
name="STRUCT" spiny="10" spinfps="6" startspin="true"
script="reset *;set specular on;select *.Cl??;spacefill 340;
select *.Na??;spacefill 230;zoom 150; 
rotate x 0;rotate y 0;rotate z 0" /> 
<noembed><a href="nacl.pdb"></a></noembed>

To create a BUTTON to highlight Na in NaCl.

<embed type="application/x-spt" width="25" height="25"
button="push" target="STRUCT"
script="reset *;set specular on; spin false; 
select *; color atoms cpk; wireframe off; spacefill off; 
select *.Na??;spacefill 160; select atomno=88; center atomno=88; 
zoom 200;rotate y 10;spacefill 200;color atoms cyan;
select *.Cl?? & within (3.0,atomno=88); color atoms darkgreen; spacefill 360;
select *.Cl?? & within (3.0,atomno=88), atomno=88" />
Highlight a Na site, CN=6

Note to get the above code to display, some '<' were converted to &l t;

11). Post your final files to your web site.

Alternative Mechanism

Use WebLabViewer to generate the data file by using the crystal builder section.
In this case, start with a simple .pdb file containing cell dimensions, space group and atomic coordinates, for example;

CRYST1    5.409    5.409    5.409  90.00  90.00  90.00 F-43m         8  1001   1
HETATM    1  S           1       1.352   1.352   1.352
HETATM    2 Zn           2        .000    .000    .000

Then from the menu, "tools", "crystal cell..." etc.
If the symmetry does NOT fit one of the 230 space groups then it may be necessary to transpose information to fit an alias, for example, VF₅ has a space group Pmnc, which is Pnma in setting b,c,a.

Return to Chemistry, UWI-Mona, Home Page

Created and maintained by Prof. Robert J. Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.

Created April 2000. Links checked and/or last modified 16th June 2006.
URL http://wwwchem.uwimona.edu.jm/courses/binsaltshow.html