There's a project for someone. I think the main problem with something like
SiO2 in quartz is that there is no specific subset of atoms that is unique
to that formula. I think a more likely alternative would be for Jmol to be
able to tell you the empirical formula of a crystal. At least for
full-occupancy structures, that might be possible.
FYI:
*Error:* I cannot find CIF file *cif/.cif* for the structure of *!*
On Tue, Sep 23, 2014 at 4:17 AM, Christian Baerlocher <
ch.baerloc...@mat.ethz.ch> wrote:
> Dear Bob,
>
> You are of course quite right, there is no SiO2 molecule, because quartz
> and all its polymorphs are „periodic nets“. You have to select a „cluster“
> and to make it neutral you would have to add terminal OH groups.
>
> This is a problem we face also in zeollite chemistry (many of them are
> polymorphs of SiO2) and a number of attempts had been made to define
> suitable clusters that describe a structure. So far the best approach for
> periodic nets seems to be that of "natural tilings“, defined and described
> by V. A. Blatov, O. Delgado-Friedrichs, M. O'Keeffe & D. M. Proserpio, Acta
> Crystallogr. A 63, 418-425 (2007). These natural tilings are further
> discussed by N. Anurova, V. A. Blatov, G. D. Ilyushin and D. M.
> Proserpio, J. Phys. Chem. C 114, 10160-10170 (2010).
>
> You can see examples of such tilings on our zeolite website. For example,
> for the natural zeolite faujasite in
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/Tilings/FAU.pdf
>
> Its framework of faujasite can be viewed with JSmol on
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_3d_JSmol.php
>
> These natural tilings have been done for all zeolites.
>
> I am not sure, if this is what Hans Horn was looking for, but it would
> certainly be nice if Jmol could display such drawings ;-)
>
> Thanks and best wishes
>
> Christian
>
>
>
> On 20 Sep 2014, at 04:24, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Well, I think it is an interesting request. Help me define what the idea
> is a bit more, and I can see what I can do. Given a few choice examples,
> how would you define your request exactly?
>
> For example, we have quartz (SiO2):
> http://chemapps.stolaf.edu/jmol/simple2.htm?load%20jsmol/data/quartz.cif%20{1%201%201}
> <http://chemapps.stolaf.edu/jmol/simple2.htm?load%20jsmol/data/quartz.cif%20%7B1%201%201%7D>
>
> In this unit cell we have
>
> Si 1 + 4(1/2) = 3 atoms
> O 6 atoms
>
> But which three atoms would you choose to represent the model for "SiO2"?
> Is it always possible to identify such a subset? Some cases probably
> involve multiple options, and they are not equivalent. For example, in this
> case, there is not a perfect tetrahedron around that Si atom. So picking
> different O atoms would give different structures for the formula unit.
> Which one would be the correct one to load? Sounds very challenging to me.
>
> Bob
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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