Bob,
The ring is flat, but it has two sp3 carbons (CH2's). To make sure this
was not associated with my post model change processing, I reproduced
the effect by building benzene from methane followed by
1,3-cyclohexadiene formation at:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
I get the same results.
My issue is fairly localized to one problem, and I'd be hesitant to
change Jmol in a way that might create more problems down the road for
this one problem. At this point, the only thing this issue is fouling is
using NIH Resolver as a "minimization" tool. It keeps returning benzene
on some modified benzene queries - most notably 1,3-cyclohexadiene.
I'm experimenting with
escape(jmolSmile.replace(/c/ig, 'C'))
on this type of query only - i.e. NIH Resolver "minimize."
I'm not sure that I'd even call this a work around since there is
nothing wrong with Jmol smiles. Playing around with benzene and pyridine
indicates that this approach is working. Even though I do not change "n"
in the 2,3-dihydropyridine query, the Resolver reads in correctly and
returns the correct SMILES and model.
The lower case Kekule aromatic SMILES will play havoc with asymmetric
"compares" - JME/Jmol & NIH/Jmol. But I'm not sure these asymmetric
"compares" are an issue, just a nuisance in constructing an internal
data base. In this latter case, one has to hand convert JME SMILES (for
example) to lower case aromatic.
Otis
Otis Rothenberger
chemagic.com
On 9/2/2010 3:09 PM, Robert Hanson wrote:
On Thu, Sep 2, 2010 at 9:17 AM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> 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 Rothenberger
chemagic.com <http://chemagic.com>
On 9/2/2010 1:52 AM, Robert Hanson wrote:
On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> 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 <http://chemagic.com>
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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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