Re: [Jmol-users] Coordination Compound Questions

[Robert H. <ha...@st...>]

Otis, I've also started the same thread at <
blu...@li...>, and I'm hoping it can be
explained to me how you do this with T-shaped, see-saw, and square pyramidal
shapes. I think perhaps the answer is going to be that you just leave out
the missing groups and use explicit [Xx@TBn] or [Xx@OHn] stereochemical
descriptors (and possibly [Xx@THn] for trigonal pyramidal). But I'm not sure
about that, because, for example:

[Fe@OH2]1234.C1.Br2.Cl3.N4

gives the warning:

WARNING: Chiral center has wrong connectivity -- ignored


at the Daylight Depict site. Hope to hear about that soon.

On Mon, Nov 15, 2010 at 12:44 AM, Otis Rothenberger
<osr...@ch...>wrote:

>  Bob,
>
> I think I see it. If I'm analyzing @ or @@, group 1 is toward me. Is that
> correct?
>
> Yes, group 1 is toward you, and the rotation about the others is the same
as depicted in the @ symbol itself -- CCW for "@" . The first and last
groups must be axial. The ones in between are the ones that are checked for
rotation order.

Notice that the way this works for SMILES generation in Jmol is that Jmol
will now first list all "components" based on atoms that have more than four
attachments. For example, a particular isomer of SF3IBrCl might be:

[S@]123456.I5.F1.Br6.F4.F3.Cl2

and a ferrocene model I have returns:

[Fe]123456789%10.[C@H]1%11[C@H]5[C@H]4[C@H]3[C@@H]%112.[C@H]6%12[C@H]%10[C@H
]9[C@H]8[C@H]7%12

That is, we're creating a "generic" n-coordinate center and then just
listing the attached components. The nice thing about this is that there's
no significance to the order of groups in the individual components -- it's
just the connection numbers 1-10 that determines the stereochemistry, and
you can have as many of these connected inorganic components as you need to
get the job done.

The success here is based on not requiring any sort of "canonical" or
"unique" SMILES description for our purposes. Jmol can match structures to
stereochemical SMILES strings as well as stereochemical SMILES strings to
stereochemical SMILES strings without any need for canonicalization. So
that's all we need.

Except for your finding a bug possibly, Jmol should now be able to match any
stereochemical SMILES involving allenyl, tetrahedral, trigonal bipyramidal,
or octahedral stereochemistry descriptors, and it will generate
stereochemical SMILES strings for structures with all of these shapes
automatically.

Bob


I'm playing around with two octahedral models and
>
> var x = compare({selected}, {not selected}, @j, 'stddev')
>
> where @j is the selected SMILES.
>
> Matches look good. What model characteristics would lead to a correct
> non-match of a say 0.2ish vs NaN - same stoichiometric formula. I'm not
> seeing a pattern.
>
>
NaN means there was not a basic nonstereochemical SMILES match in the first
place, I think.



> I do see the auto SMILES update. This time I just used the link commands
> that I have set up for model kit mode. It also auto updates on an sp3 invert
> click. Neat.
>
> The "database" that we are setting up was simply a .js JSON structure. The
> size got way out of hand, so I moved it to the server side and  write JSON
> from it as needed. I can see that I have some SMILES to change in the
> database in light of some of the things you've been doing.
>
> Otis
>
> Otis Rothenbergerchemagic.com
>
>
> On 11/14/2010 11:32 PM, Robert Hanson wrote:
>
> One correction. I had Jmol generating octahedral stereochemistry only if
> two or more trans pairs are identical. While those cases don't need @ or @@,
> one more case is like that as well -- when three of the four groups that are
> not listed first or last are identical. Also, I was forgetting that even if
> we don't need @ or @@, we still need to get the first and last groups to be
> axially related.
>
> Hurray for the SMILES "." convention!!! (Which makes this all possible.)
>
> This should be fixed now:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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