Subject: UBC software URL update
From: wai@dta.med.harvard.edu (Yu Wai Chen)
Date: 13 Nov 1996 18:02:17 GMT
Dear Crystallographers,
Please note that the official web page of the set of crystallography
tools developed at Department of Biochemistry of UBC, Vancouver:
- symmetry equivalent positions generator,
- XPLOR GUI,
- crystal packing with VRML, and
- The Java Lattice (structure visualization with Java)
has been moved to a new address effective immediately.
Please update your URL list and the new email addresses of the authors:
http://dta.med.harvard.edu/ubc/ubc.html
The old service will still be running for a while but will be terminated
anytime without notice. The authors are not affiliating with University of
British Columbia anymore and will not provide support for the software served
at the old site.
===================================================================
Yu Wai CHEN, Ph.D. Department of Microbiology
................................. & Molecular Genetics
tel: (617) 432-1931 Harvard Medical School
fax: (617) 432-0115 200 Longwood Avenue
email: wai@dta.med.harvard.edu Boston MA 02115
www: http://dta.med.harvard.edu/wai.html USA
===================================================================
Subject: Re: Solvent molecule treatment
From: wtah@chem.uwa.edu.au (William T A Harrison )
Date: Wed, 13 Nov 1996 18:59:17 GMT
Harry Powell wrote:
>Just my two penn'orth; if you have something like dichloromethane present
>in the crystal, and you have collected data at room temperature, it is
>possible (even likely) that the CH2Cl2 will diffuse out of your crystal
>during the data collection; hence, the occupancy of the solvent molecule
>will be time dependent and its effect will be different on reflections
>collected at different times through the collection. I don't know how you
>can deal with this in a rigorous way; maybe some kind of fancy weighting
>scheme could 'improve' refinement at the expense of scientific purity.
Interesting thread... A problem that zeolite crystallographers face
is the presence of extremely mobile water molecures, which
depending on conditions (humitidy, etc.) can diffuse out of the
structure, and then diffuse back in again!! At the same time,
the guest cations may rearrange themselves...
Further to Bu's remarks re H3O and NH4, in hydrated sodium
zeolites Na and H2O (sites may be partially occupied) are quite often
regarded as indistinguishable, or are probably jointly occupying the
same site. Does anybody have any recent experience in attacking
this type of problem?
Bill
Subject: Re: Solvent molecule treatment
From: wtah@chem.uwa.edu.au (William T A Harrison )
Date: Wed, 13 Nov 1996 18:59:15 GMT
>Just my two penn'orth; if you have something like dichloromethane present
>in the crystal, and you have collected data at room temperature, it is
>possible (even likely) that the CH2Cl2 will diffuse out of your crystal
>during the data collection; hence, the occupancy of the solvent molecule
>will be time dependent and its effect will be different on reflections
>collected at different times through the collection. I don't know how you
>can deal with this in a rigorous way; maybe some kind of fancy weighting
>scheme could 'improve' refinement at the expense of scientific purity.
>Dr Harry Powell
Interesting thread... Inorganic zeolite crystallographers have
similar problems with solvent/guest molecules sloshing about
the extra-framework cavities, or desorbing altogether.
A classic case is in hydrated sodium zeolites where (to a first
approximation) Na and H2O are just about indistinguishable on the
basis of bond distances, in the more open types of structures, and
probably occupy sites jointly. You could model these features with
widely differen models and arrive at the same answer (same R-factors).
Any insights as to how to attack this problem more systematically?
Charge balancing, and on a good day, TGA data should give a
reasonable idea of composition...
Bill
Subject: Re: Solvent molecule treatment
From: hewat@ill.fr (Alan Hewat)
Date: 14 Nov 1996 10:29:41 GMT
wtah@chem.uwa.edu.au (William T A Harrison ) writes:
> Further to Bu's remarks re H3O and NH4, in hydrated sodium
> zeolites Na and H2O (sites may be partially occupied) are quite often
> regarded as indistinguishable, or are probably jointly occupying the
> same site. Does anybody have any recent experience in attacking
> this type of problem?
Hi Bill ! You can of course use neutrons to distinguish between Na
and water :-) You can even vary the H/D ratio to vary the scattering.
>A problem that zeolite crystallographers face
>is the presence of extremely mobile water molecures, which
>depending on conditions (humitidy, etc.) can diffuse out of the
>structure, and then diffuse back in again!! At the same time,
>the guest cations may rearrange themselves...
And its pretty easy with neutron diffraction to freeze the sample :-)
Alan Hewat, ILL Grenoble, FRANCE (hewat@ill.fr) fax (33) 76.48.39.06
ftp://ftp.ill.fr/pub/dif http://www.ill.fr/dif/