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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