there may not be that many cumulenes in PubChem. I notice that their
substructure search for [C]=[C]=[C] fails because it tops out at 2,000,000
hits, but of course that is ridiculous.
On Mon, Dec 7, 2015 at 9:51 PM, CheMagic <osrot...@chemagic.com> wrote:
> I understand. There are lots of technical references about MMFF94 and
> allenes. Here's quick read bottom line article:
>
> http://journal.frontiersin.org/article/10.3389/fbioe.2015.00066/full
>
> I was just saying PubChem would have a lot of entries that they would have
> to change because this is universal, though one reference I read said it
> starts to get it right at high substitution.
>
> On a serious note, they evidently do make some changes at PubChem. The
> PubChem staff member that help me with the JSONP changs mentioned this as
> an aside during our email exchanges. I forget what brought it up.
>
> Otis
>
> Sent from my iPad
>
> On Dec 7, 2015, at 8:31 PM, CheMagic <osrot...@chemagic.com> wrote:
>
> Bob,
>
> Well, OK, but...
>
> 2,4-Dimethylpenta-2,3-diene
>
> (winking smiley face)
>
> It turns out the Jmoll's implementation of MMFF94 doen't
> get 2,4-Dimethylpenta-2,3-diene out of the above linear minimum - not sure
> about UFF. I have to check the docs to see how you turn UFF on. I forget.
>
> Drag/sculpt moves you toward the correct picture, but even there you're
> fighting other minimums.
>
> Otis
>
>
>
> Sent from my iPad
>
> On Dec 7, 2015, at 7:01 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> *the PubChem 3-D conformer model for a chemical structure represents all
> possible “biologically-relevant conformations that the molecule may
> have”.*Well,
> not in this case. So then it's just a bug in PubChem. Obviously allene will
> not have a flat conformation in a biological system.
>
> 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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