From owner-chemistry@ccl.net Wed Mar 11 16:50:01 2015 From: "Cina Foroutan-Nejad canyslopus---yahoo.co.uk" To: CCL Subject: CCL: Querry: Get Ring/Aromatic bonds and atom types information Message-Id: <-51109-150311160937-29593-XoD/hx10ws1Pgm8iiiAYnw[#]server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="----=_Part_4912432_1148754.1426104504532" Date: Wed, 11 Mar 2015 20:08:24 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus/./yahoo.co.uk] ------=_Part_4912432_1148754.1426104504532 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Everything that is related to chemical bond is potentially controversial! H= ere is my suggestion. I assume by "rotatable bond" you mean single bond. So= , you need a tool to discriminate between single, double, triple, etc. bond= s. 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 y= ou can check some nice books by Richard Bader, Paul Popelier or a newer boo= k by Cherif Matta in which full description is given.The other tool which i= s not much inexpensive but really robust is "delocalization index". For a b= rief 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 ni= ce software packages for computation of ellipticity or delocalization index= :http://multiwfn.codeplex.com/http://aim.tkgristmill.com/ Good luck,Cina --------------------------------------------------------------------Cina Fo= routan-Nejad, PhDCEITEC-Central European Institute of Technology,Masaryk Un= iversity, Brno,Czech Republichttps://muni.academia.edu/CinaForoutanNejad =20 On Wednesday, 11 March 2015, 21:05, Cina Foroutan-Nejad wrote: =20 Everything that is related to chemical bond is potentially controversial! = Here is my suggestion. I assume by "rotatable bond" you mean single bond. S= o, you need a tool to discriminate between single, double, triple, etc. bon= ds. 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 bo= ok 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, 63= 3/ChemPhysChem, 2013, 14,1211/Chem. Eur. J. 2014, 20, 10140.Here are some n= ice software packages for computation of ellipticity or delocalization inde= x:http://multiwfn.codeplex.com/ AIMAll | =C2=A0 | | =C2=A0 | =C2=A0 | =C2=A0 | =C2=A0 | =C2=A0 | | AIMAllCopyright =C2=A9 by Todd A. Keith 1997-2014 (aim]![tkgristmill.com) = | | | | View on aim.tkgristmill.com | Preview by Yahoo | | | | =C2=A0 | =C2=A0=20 On Wednesday, 11 March 2015, 20:44, Gulzar Singh gulzar.singh54]*[gmai= l.com wrote: =20 =20 Sent to CCL by: "Gulzar=C2=A0 Singh" [gulzar.singh54- -gmail.com] Hi I need to get information about rotatable bonds only, from a given structur= e. Basic idea to get this information is to remove rings and other double/trip= le bonds or directly detect rotatable bonds. eg: from this N[C]*[]*[H](CC1=3DCN=3DCN1)C(O)=3DO , there are only 3 rotata= ble bonds and one ring. But how to get this information computationally? Which software/tool/package/algorithm can provide this information along wi= th the type of atom (C, N, O etc.) and its position (C1, N3, C4 etc.). Pyth= on tool is preferred. Thank You -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 ------=_Part_4912432_1148754.1426104504532 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Ev= erything that is related to chemical bond is potentially controversial! Her= e 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. T= he 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.
T= he other tool which is not much inexpensive but really robust is "delocaliz= ation index". For a brief introduction you may see these papers:
Coord. Chem. Rev. 2005, 249, 633/ChemPhysChem, 2013, 14,1211/Ch= em. Eur. J. 2014, 20, 10140.
Here are some nice softw= are packages for computation of ellipticity or delocalization index:
<= div dir=3D"ltr" id=3D"yiv7690906230yui_3_16_0_1_1426093914710_42447" class= =3D"" style=3D"">http://multiwfn.= codeplex.com/

Good luck,
Cina

---------= -----------------------------------------------------------
Cina Foroutan-Nejad, PhD
CEITEC-Central Euro= pean Institute of Technology,
Masaryk University, Brn= o,
Czech Republic


<= div dir=3D"ltr"> On Wednesday, 11 March 20= 15, 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 ass= ume by "rotatable bond" you mean single bond. So, you need a tool to discri= minate between single, double, triple, etc. bonds. As a QTAIM fan, I know t= wo 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 man= y papers by Richard Bader about ellipticity or you can check some nice book= s 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, 14,1= 211/Chem. Eur. J. 2014, 20, 10140.
Here are some nice software packages for= computation of ellipticity or delocalization index:
<= /tr>=
 
 
 
 
 <= /div>
 
AIMAll
Copyright =C2=A9 by Todd A. Keith 19= 97-2014 (aim]![tkgristmill.com)
View on a= im.tkgristmill.com
Preview by Yah= oo
 
 


<= div dir=3D"ltr"> On Wednesday, 11 March 20= 15, 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 b= onds only, from a given structure.
Basic idea to get this= information is to remove rings and other double/triple bonds or directly d= etect rotatable bonds.
eg: from this N[C]*[]*[H](CC1=3DCN= =3DCN1)C(O)=3DO , 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.). Py= thon tool is preferred.

Thank You



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