Hi James,
They're two separate things.
One is a connectivity analysis that looks at whether the way the structure
is connected would make it possible for rotation to occur about a bond,
regardless of what sort of bond that could be.
The second involves categorising an individual bond and then looking at the
energetic cost of rotating a bond of that type.
If a bond is part of a 5-membered ring, then there is no way rotation about
it can occur, regardless of whether it is single, double, etc.
Best wishes,
Jens
On 17 September 2014 22:36, James Mao <xjames...@gmail.com> wrote:
> Oh you must be right. I have no knowledge about this.
>
>
>
> Just out of curiosity, in topological sense, if a bond order is between 1
> and 2 (due to conjugation for example), will it be considered as rotatable?
>
>
>
> Best wishes,
>
> James
>
>
>
> *From:* Jens Thomas [mailto:jenstho...@users.sourceforge.net]
> *Sent:* Wednesday, September 17, 2014 3:25 PM
> *To:* avogadro-discuss@lists.sourceforge.net
> *Subject:* Re: [Avogadro-Discuss] How to calculate rotateable bonds?
>
>
>
> I think Max meant which bonds are rotatable in a topological sense - i.e.
> are not part of a ring and so the two parts of the molecule are free to
> move.
>
>
>
> I think this code lives in openbabel. The following source file might be a
> good place to start:
>
>
>
>
> http://sourceforge.net/p/openbabel/code/HEAD/tree/openbabel/trunk/src/rotor.cpp
>
>
>
> I've not had a chance to look here myself, but I think the CDK also has
> code for ring perception:
>
>
>
> http://sourceforge.net/projects/cdk/
>
>
>
> Best wishes,
>
>
>
> Jens
>
>
>
>
>
> On 17 September 2014 20:08, James Mao <xjames...@gmail.com> wrote:
>
> Isn’t that you need define “rotatable” first? A rotational barrier below a
> limit? Then you need define it is a rigid rotation or relaxed rotation, at
> what computational level…
>
> I don’t think this is what Avogadro should consider, but you can do it by
> yourself.
>
>
>
> James Mao
>
> ---------------------------------------
>
> Postdoctoral Research Associate
>
> 1207 Chevron Science Center,
>
> Department of Chemistry,
>
> University of Pittsburgh
>
>
>
> *From:* Maxwell Wesley Terban [mailto:mwt2...@columbia.edu]
> *Sent:* Tuesday, September 16, 2014 3:16 AM
> *To:* avogadro-discuss@lists.sourceforge.net
> *Subject:* [Avogadro-Discuss] How to calculate rotateable bonds?
>
>
>
> Hi,
>
> I am wondering how Avogadro computes rotateable bonds in a molecule. I
> want to write my own code in python to do something similar in which I
> would input a molecular structure and then the program would categorize and
> print out which bonds in the structure are rotateable.
>
> Thanks,
> Max
>
>
>
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