From owner-chemistry@ccl.net Wed Mar 11 06:44:00 2015 From: "Christina MSC christinamsc*_*gmail.com" To: CCL Subject: CCL: How to calculate solvation energy Message-Id: <-51105-150311064224-20801-Fd0iIj5/vXirgw/6E0RDpQ- -server.ccl.net> X-Original-From: "Christina MSC" Date: Wed, 11 Mar 2015 06:42:17 -0400 Sent to CCL by: "Christina MSC" [christinamsc[]gmail.com] Dear All, I am dealing with the metal complexes having seven coordination. In this complexes the seventh coordination will be the solvent. I would like to know how to calculate the role of this solvent coordinated in this complexes. I will also know how to calculate the solvation energy of this complexes. I would be happy if anyone explains briefly. Thanks in advance. Christina From owner-chemistry@ccl.net Wed Mar 11 13:30:01 2015 From: "Mehdi Esrafili m_esrafili]|[yahoo.com" To: CCL Subject: CCL:G: How to do EDA (energy decomposition analysis using gaussian g09? Message-Id: <-51106-150311022139-3583-Qeq2PvqHHvZSyYrXLgBONA]_[server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="----=_Part_3406366_1017817141.1426054890536" Date: Wed, 11 Mar 2015 06:21:30 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili:yahoo.com] ------=_Part_3406366_1017817141.1426054890536 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Shawkat;There is no possibility for EDA calculations in G09. However, = you can do this by GAMESS-UK package.=20 =C2=A0=C2=A0---------------------------------------------------------------= ---------------------------------------------------------------=C2=A0=C2=A0= `The man who makes no mistakes does not usually make anything.'=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Edward John Phelps (1822-1900)--------= ---------------------------------------------------------------------------= -------------------------------------------=20 Mehdi D. Esrafili, Ph.D.Assistant Professor of Physical Chemistry=C2=A0 Current address:=C2=A0Department of Chemistry, Faculty of Basic Sciences,Un= iversity ofMaragheh, Iran. E-mail 1: m_esrafili]![yahoo.com=20 E-mail 2: esrafili]![maragheh.ac.ir------------------------------------------= ---------------------------------------------------------------------------= --------- =20 On Wednesday, March 11, 2015 7:07 AM, Shawkat Islam sislam:-:swin.edu.= au wrote: =20 =20 Sent to CCL by: "Shawkat=C2=A0 Islam" [sislam%swin.edu.au] Hello CCL users, I want to use energy decomposition analysis based on the atom fragmentation= =20 in gaussian g09. Can anybody tell me how to do it? What is the keyword? Thanks Shawkat Australia -=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------=_Part_3406366_1017817141.1426054890536 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Shawkat;
There is no possibility for EDA calculations = in G09. However, you can do this by GAMESS-UK package.
 
 
------------------------------------------------------------= ------------------------------------------------------------------ &nb= sp;
`The man who makes no mistakes does not usually make anythin= g.'
          =             &nb= sp;           Edward John= Phelps (1822-1900)
--------------------------------------------= ---------------------------------------------------------------------------= -------
Mehdi D. Esrafili, Ph.D.
Assistant Professor of Phys= ical Chemistry 
Current a= ddress: Department of Chemistry,
Faculty of Basic Sc= iences,University of
Maraghe= h, Iran.
E-mail 1: m_esrafili]![yahoo.com<= font color=3D"#0080ff">
E-mail 2: esrafili]![m= aragheh.ac.ir
<= font face=3D"arial, helvetica, sans-serif">-----------------------------------= ---------------------------------------------------------------------------= ----------------


<= div style=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, = Lucida Grande, sans-serif; font-size: 12px;">
On Wed= nesday, March 11, 2015 7:07 AM, Shawkat Islam sislam:-:swin.edu.au <owne= r-chemistry]![ccl.net> wrote:



Sent to CCL by: "Shawkat  Islam" [sislam%swin.edu.= au]
Hello CCL users,

I want to use energy decomposition analysis = based on the atom fragmentation
in gaussian g09.

Can anybody tel= l me how to do it? What is the keyword?


Thanks
Shawkat
Aus= tralia



-=3D This is automatically added to each message by t= he mailing script =3D-
To recover the email address of the author of the= message, please change
the strange characters on the top line to the ]![ = sign. You can also
E-mail to subscribers: CHEMISTRY]![ccl.net or use:
   = ;   http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-ma= il to administrators: CHEMISTRY-REQUEST]![ccl.net or use<= br>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /a>
     
http://www.ccl.n= et/chemistry/sub_unsub.shtml

Before posting, check wait time at:= http://www.ccl.net
Job: http://www= .ccl.net/jobs
Conferences: http://server.ccl.net/chem= istry/announcements/conferences/

Search Messages: http://w= ww.ccl.net/chemistry/searchccl/index.shtml

If your mail bounces = > from CCL with 5.7.1 error, check:
      http://www.ccl.net/spammers.tx= t

RTFI: http://www.ccl.net/chemistry/aboutccl/instruction= s/




------=_Part_3406366_1017817141.1426054890536-- From owner-chemistry@ccl.net Wed Mar 11 14:05:01 2015 From: "Gulzar Singh gulzar.singh54]*[gmail.com" To: CCL Subject: CCL: Querry: Get Ring/Aromatic bonds and atom types information Message-Id: <-51107-150311054212-3510-1kRxxUwPnFP7nSj2R5qDJA++server.ccl.net> X-Original-From: "Gulzar Singh" Date: Wed, 11 Mar 2015 05:42:10 -0400 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 From owner-chemistry@ccl.net Wed Mar 11 15:16:01 2015 From: "may abdelghani may01dz::yahoo.fr" To: CCL Subject: CCL:G: Re : CCL:G: How to do EDA (energy decomposition analysis using gaussian g09? Message-Id: <-51108-150311151156-30910-IUvi+NwhUtjJ9X94q3glPw(a)server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 11 Mar 2015 19:11:47 +0000 MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz_-_yahoo.fr] yes you can do and EDA calculation with G09 but with the help of AOMix: http://www.sg-chem.net/aomix/ Look in AOMix manual page 37 ; Good luck -------------------------------------------- En date de : Mer 11.3.15, Shawkat Islam sislam:-:swin.edu.au a écrit : Objet: CCL:G: How to do EDA (energy decomposition analysis using gaussian g09? À: "Abdelghani, May " Date: Mercredi 11 mars 2015, 3h00 Sent to CCL by: "Shawkat  Islam" [sislam%swin.edu.au] Hello CCL users, I want to use energy decomposition analysis based on the atom fragmentation in gaussian g09. Can anybody tell me how to do it? What is the keyword? Thanks Shawkat Australia                     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 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



-=3D= This is automatically added to each message by the mailing script =3D-
To recover the email address of the author of the message, p= lease change
the strange characters on the top line to th= e ]![ sign. You can also
look up the X-Original-From: line = in the mail header.

E-mail to subscrib= ers: CHEMISTRY]![ccl.net= or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]![ccl.net or us= e
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

    &nbs= p; http://www.ccl.net/chemistry/sub_unsub.s= html

Before posting, check wait ti= me at: http://www.ccl.net

J= ob: http://www.ccl.net/jobs
Conferences: = http://server.ccl.net/chemist= ry/announcements/conferences/

Sear= ch Messages: http://www.ccl.net/chemi= stry/searchccl/index.shtml

If your= mail bounces from CCL with 5.7.1 error, check:
  &n= bsp;   http://www.ccl.net/spammers.txt

RTFI: h= ttp://www.ccl.net/chemistry/aboutccl/instructions/



<= /div>


= ------=_Part_4912432_1148754.1426104504532--