How to calculate rotateable bonds?

General Discussion
1

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

2

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:mwt2115@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

3

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:

Best wishes,

Jens

On 17 September 2014 20:08, James Mao xjamesmao@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:mwt2115@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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4

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:jensthomas@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:

Best wishes,

Jens

On 17 September 2014 20:08, James Mao xjamesmao@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:mwt2115@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

Want excitement?
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When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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5

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 xjamesmao@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:jensthomas@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:

Open Babel / Code / [r5041] /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:

The Chemistry Development Kit download | SourceForge.net

Best wishes,

Jens

On 17 September 2014 20:08, James Mao xjamesmao@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:mwt2115@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

Want excitement?
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When you want reliability, choose Perforce
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Perforce version control. Predictably reliable.

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6

Hi Jens,

Thank you very much.

So for the function Max is looking for or similar functions, we usually can find

them under “Plugins” menu from OpenBabel, right? Never noticed them before,

and they are very helpful.

Thanks again.

Best,

James

From: Jens Thomas [mailto:jensthomas@users.sourceforge.net]
Sent: Thursday, September 18, 2014 4:43 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] How to calculate rotateable bonds?

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 xjamesmao@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:jensthomas@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:

Best wishes,

Jens

On 17 September 2014 20:08, James Mao xjamesmao@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:mwt2115@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

Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191 http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk &iu=/4140/ostg.clktrk

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Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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7

Some simple rules such as based on the connected atom types could be useful, please see Makino &Kuntz, J. Comp. Chem., 18 (1997), p 1812-25. (You must have a mol2 file of the molecule.)

Actually based on those rules, many years ago I wrote a Perl script http://www.ccl.net/cca/software/PERL/Find_Rotatable_Bonds/findrotatable.pl, also in https://github.com/UnixJunkie/findrotatable.

Vis