Subject: Re: CCL:CRYSTAL03 -

From: "Dr. Alexander Hofmann" <ah #%# chemie.hu-berlin.de>
Date: Mon, 20 Jun 2005 10:24:02 +0200

Hello,

> What now bothers me about the present structure is that using a 
> visualisation package I see something not resembling crystal at all!

I've tried to setup the monoclinic crystal with Cerius2. It does not look like a crystal. So I think that either positions or spacegroup or both is wrong. I'd suggest to check a database or the original work for that.

> Reasons why the geometry inputs cannot be wrong are: (i) I've used 
> different sets of well documented theoretical and experimental 
> geometrical inputs with the same result (ii) other geometries for other 
> different structures, other space groups, are very much perfect and 
> gives me the right crystals.
> My guess is (i) there is a bug in the crystal03 code as pertains to 
> space group 11, but I've been assured that crystal03 code space group is 
> bugfree (ii) maybe the structure(Na3AlH6) was assigned the wrong space 
> group.
Hm, may be, but as long crystal _and_ cerius2 gives the same (wrong) answer I'd like to search the error on the input side.
Do you have a publication which gives _all_ positions of the atoms in the cell? Including the one generated by symmetry? This may help us.

Alex

-- 

Dr. Alexander Hofmann

Humboldt-Universitaet zu Berlin
Institut fuer Chemie
Arbeitsgruppe Quantenchemie

Post:     Unter den Linden 6      
          10099 Berlin              
Visitors: Brook-Taylor-Strasse 2 
          12489 Berlin

ah #%# chemie.hu-berlin.de

Tel.: +49-30-2093-7138
Fax.: +49-30-2093-7136

http://www.chemie.hu-berlin.de/ag_sauer/index.html

PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35

---

From: Jacco van de Streek <streek/at/ccdc.cam.ac.uk>
Date: Mon, 20 Jun 2005 11:46:18 +0100

(The short answer is: you input the incorrect space group. Both the 
published Na3AlH6 crystal structure and the CRYSTAL03 program are fine. 
See below for the long answer.)

Ojwang, J.G.O. wrote:
> The geometry I used are as follows:
> 
> (a =5.33, b=5.53, c=7.68, beta=90.103)(space group(P21/n) 11)

Space-group number 11 is P21/m, not P21/n. Or, to put it the opposite 
way round, P21/n is space-group number 14, not space-group number 11.

> Al  0.0   0.0   0.0
> Na  0.0   0.0   0.5
> H 0.9897 0.4532 0.2535
> H 0.2281 0.3307 0.5437
> H 0.1608 0.2673 0.9366

In both P21/m and P21/n Al and Na with these coordinates would be on a 
special position with a multiplicity of 2. It is therefore not possible 
that these coordinates ever generate a stoichiometry of Na3AlH6: you're 
at least one sodium atom (not in a special position) short.

I took the coordinates from the attachment called ccl2.in by Dr 
Alexander Hofmann. If I combine his coordinates with the symmetry 
operators for P21/n (space-group number 14, unique axis b, cell choice 
2) I get a crystal structure that does not have any close contacts / 
short bonds, that has the correct soichiometry and in which the aluminum 
(and sodium) is symmetrically coordinated by six hydrogens.

I have attached a .res file. This file format has the advantage that it 
only allows you to specify the symmetry operators explicitly (albeit in 
condensed form). You can view this crystal structure in various 
programs, in our freely available visualiser Mercury (available for a 
variety of platforms) for example:

http://www.ccdc.cam.ac.uk/products/csd_system/mercury/

Mercury can also write out the file in other formats, like .mol2, and it 
can display the full list of symmetry operators.

I wanted to check that the supercell structure was still the same as the 
P41/a structure by comparing the simulated powder difraction patterns, 
but as far as I can tell the P41/a structure in Alexander Hofmann's 
second attachment is missing a sodium atom again, and some hydrogens 
this time. If you have the P41/a structure, you can simulate the powder 
diffraction patterns yourself using Mercury.

Best wishes,
-- 
Dr Jacco van de Streek
Research Scientist
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom
TITL CCL
CELL 0.71073 5.33 5.53 7.68 90 90.103 90
ZERR 4 0.000 0.000 0.000 0 0.000 0
LATT 1
SYMM 1/2-x,1/2+y,1/2-z
SFAC H Na Al
UNIT 12 6 2
FVAR 1.00
Al      3  0.000000  0.000000  0.000000  0.500000 0.05
Na      2  0.000000  0.000000  0.500000  0.500000 0.05
H1      1  0.100000  0.048100  0.216400  1.000000 0.05
H2      1  0.228100  0.330700  0.543700  1.000000 0.05
Na      2 -0.010300  0.453200  0.253500  1.000000 0.05
H3      1  0.160800  0.267300 -0.063400  1.000000 0.05
END