Thanks Otis, you've given me a lot of food for thought.
I guess just about every concept/model/language system we use faces this
kind of difficulty. Even the idea of a molecule is extremely difficult to
define precisely, but is rarely troublesome in practice. Similarly, I would
suggest that the great majority of ring systems are readily classified as
aromatic, or not aromatic, and the troublesome cases are relatively few in
number, though very interesting. In education, it seems reasonable to
introduce learners to clear-cut examples at first, and reveal problematic
cases later. It is from from that pragmatic perspective that I asked if
Jmol could be used to 'pass judgement' on whether structures were aromatic
or not, and to give its reasons.
As regards intelligent feedback, I think there is great untapped potential
to use the cheminformatics tools now at our disposal to build online
tutorial resources that respond intelligently and flexibly to user input.
The SMILES/SMARTS capabilities in Jmol, and the wide variety of other free
Javascript tools for chemistry, are very promising in that respect.
With thanks,
Mike
Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420
On 16 May 2016 at 20:27, Otis Rothenberger <osrot...@icloud.com> wrote:
> Mike,
>
> Although it’s not in the Resolver docs, Resolver can do this (below). This
> is all going to be dependent on CATVS aromatic SMILES rules. Notice that
> Oc1ccccc1
> <https://cactus.nci.nih.gov/chemical/structure/Oc1ccccc1/aromatic> and
> C1=CC=CC(O)=C1
> <https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic> are
> both recognized as aromatic, consistent with another bit of old wisdom on
> the Daylight site:
>
> When should I specify a structure as aromatic?
>
> You never need to do so. If you find yourself typing in SMILES, it's a bit
> easier to type "c1ccccc1" for benzene instead of "C1=CC=CC=C1"
> cyclohexatriene, but it's just a matter of convenience, since they
> mean exactly the same thing.
>
> https://cactus.nci.nih.gov/chemical/structure/cyclohexane/aromatic NO
>
> https://cactus.nci.nih.gov/chemical/structure/phenol/aromatic YES
>
> https://cactus.nci.nih.gov/chemical/structure/Oc1ccccc1/aromatic YES
>
> https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic
> YES
>
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On May 16, 2016, at 1:49 PM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
> Mike,
>
> The idea of “intelligent” feedback is intriguing. We played around with
> this concept in a large section at ISU years ago. It was fun, but
> frustrating! I don’t know if Bob can do what you ask with Jmol SMILES or
> not. For my part, I learned two things form this email chain:
>
> 1) It forced me to look at Bob’s SMILES/SMARTS docs, and I now understand
> why cyclopentadienone is aromatic - or not depending on the Jmol SMILES
> setting!
>
> 2) I also learned that Daylight had a sense on humor on the subject at
> hand. From their docs:
>
> QUOTE
> What does "aromatic" mean, anyway?
>
> "Aromatic" means "it smells nice". No kidding, that's the only defensible
> definition. There is no single rigorous definition of aromaticity in
> chemistry. To a synthetic chemist, aromaticity implies something
> about reactivity; to a thermodynamicist, about heat of formation; to a
> spectroscopist, about NMR ring current; to a molecular modeler, about
> geometrical planarity; to a cosmetic chemist, it probably means "smells
> nice". The SMILES definition of aromaticity has nothing to do with the
> other definitions, except that we'd all agree that benzene is "aromatic".
> END QUOTE
>
> In a 2007 blog, Rich Apodaca (ChemWriter Application) took a look at the
> history of SMILES and aromaticity. It’s an interesting read:
>
> http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-broken/
>
> Otis
>
>
>
>
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