CCL: Querry: Get Ring/Aromatic bonds and atom types information
- From: Cina Foroutan-Nejad <canyslopus###yahoo.co.uk>
- Subject: CCL: Querry: Get Ring/Aromatic bonds and atom types
information
- Date: Wed, 11 Mar 2015 20:08:24 +0000 (UTC)
Everything that is related to chemical bond is potentially controversial!
Here is my suggestion. I assume by "rotatable bond" you mean single
bond. So, you need a tool to discriminate between single, double, triple, etc.
bonds. As a QTAIM fan, I know two different tools within the context of theory.
The easy, inexpensive, but not 100% reliable tool is bond ellipticity at (3, -1)
CP. You can find many papers by Richard Bader about ellipticity or you can check
some nice books by Richard Bader, Paul Popelier or a newer book by Cherif Matta
in which full description is given.The other tool which is not much inexpensive
but really robust is "delocalization index". For a brief introduction
you may see these papers:Coord. Chem. Rev. 2005, 249, 633/ChemPhysChem, 2013,
14,1211/Chem. Eur. J. 2014, 20, 10140.Here are some nice software packages for
computation of ellipticity or delocalization index:http://multiwfn.codeplex.com/http-:-//aim.tkgristmill.com/
Good luck,Cina
--------------------------------------------------------------------Cina
Foroutan-Nejad, PhDCEITEC-Central European Institute of Technology,Masaryk
University, Brno,Czech Republichttps://muni.academia.edu/CinaForoutanNejad
On Wednesday, 11 March 2015, 21:05, Cina Foroutan-Nejad
<canyslopus]![yahoo.co.uk> wrote:
Everything that is related to chemical bond is potentially controversial! Here
is my suggestion. I assume by "rotatable bond" you mean single bond.
So, you need a tool to discriminate between single, double, triple, etc. bonds.
As a QTAIM fan, I know two different tools within the context of theory. The
easy, inexpensive, but not 100% reliable tool is bond ellipticity at (3, -1) CP.
You can find many papers by Richard Bader about ellipticity or you can check
some nice books by Richard Bader, Paul Popelier or a newer book by Cherif Matta
in which full description is given.The other tool which is not much inexpensive
but really robust is "delocalization index". For a brief introduction
you may see these papers:Coord. Chem. Rev. 2005, 249, 633/ChemPhysChem, 2013,
14,1211/Chem. Eur. J. 2014, 20, 10140.Here are some nice software packages for
computation of ellipticity or delocalization index:http://multiwfn.codeplex.com/
AIMAll
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On Wednesday, 11 March 2015, 20:44, Gulzar Singh gulzar.singh54]*[gmail.com
<owner-chemistry]![ccl.net> wrote:
Sent to CCL by: "Gulzar Singh" [gulzar.singh54- -gmail.com]
Hi
I need to get information about rotatable bonds only, from a given structure.
Basic idea to get this information is to remove rings and other double/triple
bonds or directly detect rotatable bonds.
eg: from this N[C]*[]*[H](CC1=CN=CN1)C(O)=O , there are only 3 rotatable bonds
and one ring.
But how to get this information computationally?
Which software/tool/package/algorithm can provide this information along with
the type of atom (C, N, O etc.) and its position (C1, N3, C4 etc.). Python tool
is preferred.
Thank You
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