On Thu, Sep 2, 2010 at 9:17 AM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> Bob,
>
> Thanks. Your explanation of what aromatic means is the key here. I see now
> why this is happening. If I start with benzene and make 1,3-cyclohexadiene,
> then it ends up in flat energy minimum that "minimize" does not change. I
> always get the lower case smiles. If I use "drag" to pull it out of shape,
> then I get upper case. If I make cyclohexene from benzene, "minimize"
> eventually get it and twists a bit. Once it twists, I get upper case.
>
> One thing here is that it looks like the statement "aromatic just means
> flat and all sp2 for Jmol" is not quite correct. Flat seems to be a
> sufficient condition.
>
then there's a bug. You sure you have a tetrahedral center? -- not just
"square planar but distorted square planar"?
>
> The context here may seem strange, but we are working on student model kit
> exercises, and we want the Jmol model kit to allow the same kind on tactile
> playing that a ball and stick model kit allows - e.g. take a double bond out
> of benzene. To be sure, I do not see the problem if I make
> 1,3-cyclohexadiene from cyclohexane. That should have been a clue that the
> flatness was the issue!
>
> Re NIH, for all of the following, the Resolver returns benzene (no explicit
> hydrogens in submitted SMILES):
>
> Jmol lower case benzene
> Jmol lowercase cyclohexadiene
> Jmol lower case cylohexene
> Jmol lower case cyclohexane, which is, of course synonymous with "aromatic
> SMILES" for benzene.
>
> Evidently, the Resolver is just ignoring "=" in this lower case context.
>
>
that makes sense. What do you propose? There could be an aromatic option
that requires explicit hydrogens:
/explicitaromatic/
--- flat ring
--- tricoordinate carbon
--- all substituents in plane of ring
/aromatic/ (default)
-- flat ring
-- all substituents in plane of ring
I hate to think what implications it might have for heterocycles, though.
That's what I was trying to avoid.
Bob
> Otis
>
> Otis Rothenbergerchemagic.com
>
>
> On 9/2/2010 1:52 AM, Robert Hanson wrote:
>
>
>
> On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger
> <osrot...@chemagic.com>wrote:
>
>> Bob,
>>
>> There is a general aromatic problem that I'm having with find SMILES
>> that's easiest to explain with a specific scenario. If I load benzene
>> and run "var x={*}.find('SMILES');echo @x," I get:
>>
>> c1=cc=cc=c1
>>
>> If I use model kit mode to make 1,3-cyclohexadiene, the same "var
>> x={*}.find('SMILES');echo @x" produces
>>
>> c1=cc=ccc1
>>
>>
> I'll look into that. Almost certainly a bug. It should only use lower case
> c if the ring is totally flat and there are no sp3 centers. I'm really
> surprised it's doing that. The code is only supposed to insert lower case
> "c" when:
>
> -- the ring is flat
> -- the ring has no sp3 centers
>
> Is it possible you are sending it a flat no-hydrogen ring? When I use the
> model kit, I get:
>
>
> C1=CCCC=C1
>
>
>
>
>> I'm now stuck in lower case "c" mode on this ring no matter what I do to
>> the ring. If I break a ring bond while the ring is no longer aromatic
>> and reform the bond, I go back to upper case "C"
>>
>>
> remember -- "aromatic" just means "flat and all sp2" for Jmol. We're not
> going to get into multiple bonding issues. There's no "antiaromatic" here.
> It doesn't matter if you have 6 carbons and all single bonds or 6 carbons
> and all double bonds or 8 carbons (as in octadienyl dianion ligand). As long
> as it's flat and there aren't any tetrahedrally directed substituents, Jmol
> is going to use "c" instead of "C".
>
> Bob
>
>
>
>> There are really two issues here:
>>
>> 1) Jmol creates Kekule SMILES in lower case, and this does not seem to
>> be standard. As long as compare is Jmol/Jmol, this is not a problem. And
>> in fact, NIH Resolver which uses aromatic SMILES (c1ccccc1), recognizes
>> the Jmol lower case Kekule SMILES for benzene.
>>
>
> It's definitely incorrect. You really have all the H atoms there and it's
> not planar?
>
> 2) Getting stuck in lower case mode, however, is a problem and seems to
>> be a bug.
>>
>> I have a feeling that calculate/reset aromatic may offer one solution to
>> the problem, but I'm not sure it can be used in a general sense to
>> "unaromatise" an aromatic ring. If this is not a bug, an alternative is
>> to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
>> side affects.
>>
>>
> See if you can find out more about what exactly the NIH server is
> requiring, if that's the issue. There's also a
>
> /noaromatic/ flag in Jmol's SMILES business that turns off aromatic
> checking. That might be useful.
>
> Help me define what the context is. Where are these being used?
>
>
>
>> Otis
>>
>> --
>> Otis Rothenberger
>> chemagic.com
>>
>>
>>
>>
>>
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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
>
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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
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