From owner-chemistry@ccl.net Wed Aug 22 04:18:01 2012 From: "=?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= gjgarcia:ujaen.es" To: CCL Subject: CCL:G: Restart ONIOM optimization from chk file Message-Id: <-47443-120822041327-17326-nsoB1ZKJYpcdSYSVns4vlQ:_:server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 22 Aug 2012 10:13:05 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= [gjgarcia~~ujaen.es] Hi Could I restart an oniom optimization from chk file in Gaussian? How i do it? I have tried with opt=restart, but all system (low, medium and high layers) is placed as high level, i.e. it tries to optimize all system at the high level. Thanks in advance -- Gregorio García Moreno From owner-chemistry@ccl.net Wed Aug 22 04:52:01 2012 From: "Sergio Manzetti sergio.manzetti:_:gmx.com" To: CCL Subject: CCL: Electronnegativity and QM Message-Id: <-47444-120822044039-25791-indCa2ndWe/S4o0TmnHTEQ/a\server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167001345624829464220" Date: Wed, 22 Aug 2012 10:40:29 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#%#gmx.com] --========GMXBoundary167001345624829464220 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs, how can one show the cumulative electronnegative effect from a molecule using quantum mechanical calculations? Considering for instance SF6 which fluor atoms exert a strong electronnegative force from the nucleus in the van der Waal and Coulombic environment. Is it from a regular electrostatic mapping? Thanks Sergio --========GMXBoundary167001345624829464220 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs, how can one show the cumulative electronnegative effect from a molecule= using quantum mechanical calculations? Considering for instance SF6 which = fluor atoms exert a strong electronnegative force from the nucleus in the v= an der Waal and Coulombic environment. Is it from a regular electrostatic m= apping?
=20
=20 Thanks
=20
=20 Sergio
=20
=20 --========GMXBoundary167001345624829464220-- From owner-chemistry@ccl.net Wed Aug 22 10:06:00 2012 From: "W.M. Chamil Sameera wsameera!^!ICIQ.ES" To: CCL Subject: CCL:G: Restart ONIOM optimization from chk file Message-Id: <-47445-120822055739-9156-+Ba3Dkx1C8WC5jJIHlha7w()server.ccl.net> X-Original-From: "W.M. Chamil Sameera" Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 22 Aug 2012 09:56:24 +0000 MIME-Version: 1.0 Sent to CCL by: "W.M. Chamil Sameera" [wsameera[a]ICIQ.ES] Hi Gregorio, Yes, opt=restart can RESTART ONIOM(QM:MM) structure optimization, where Gaussian09 can recover information. Not sure why it does not work for you. Simple test: Does Gaussian report ONIOM extrapolated energy at each optimization step after RESTART? Sameera. ..... Dr. W. M. C. Sameera Institut Català d’Investigació Química (ICIQ) Av. Països Catalans 16 – 43007 Tarragona Tel +34 977920229 Fax +34 977920231 Web: http://www.iciq.es/ ________________________________________ > From: owner-chemistry+wsameera==iciq.es|ccl.net [owner-chemistry+wsameera==iciq.es|ccl.net] on behalf of Gregorio García Moreno gjgarcia:ujaen.es [owner-chemistry|ccl.net] Sent: 22 August 2012 10:13 To: W.M. Chamil Sameera Subject: CCL:G: Restart ONIOM optimization from chk file Sent to CCL by: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= [gjgarcia~~ujaen.es] Hi Could I restart an oniom optimization from chk file in Gaussian? How i do it? I have tried with opt=restart, but all system (low, medium and high layers) is placed as high level, i.e. it tries to optimize all system at the high level. Thanks in advance -- Gregorio García Morenohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Aug 22 13:21:00 2012 From: "Amir Bernat bernat]^[post.bgu.ac.il" To: CCL Subject: CCL:G: Restart ONIOM optimization from chk file Message-Id: <-47446-120822131928-12198-fA+22vO2sbYOEdAewBZhOw%%server.ccl.net> X-Original-From: Amir Bernat Content-Type: multipart/alternative; boundary=20cf300faad5a0502904c7ddf1c5 Date: Wed, 22 Aug 2012 20:19:22 +0300 MIME-Version: 1.0 Sent to CCL by: Amir Bernat [bernat:+:post.bgu.ac.il] --20cf300faad5a0502904c7ddf1c5 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Have you added "guess=3Dread"? I use this on DFT calculations figured iy should work for you as well, just make sure you keep the original .chk file. Amir On Wednesday, August 22, 2012, W.M. Chamil Sameera wsameera!^!ICIQ.ES < owner-chemistry]=[ccl.net> wrote: > > Sent to CCL by: "W.M. Chamil Sameera" [wsameera[a]ICIQ.ES] > Hi Gregorio, > > Yes, opt=3Drestart can RESTART ONIOM(QM:MM) structure optimization, wher= e Gaussian09 can recover information. Not sure why it does not work for you. > > Simple test: Does Gaussian report ONIOM extrapolated energy at each optimization step after RESTART? > > Sameera. > > ..... > Dr. W. M. C. Sameera > Institut Catal=E0 d=92Investigaci=F3 Qu=EDmica (ICIQ) > Av. Pa=EFsos Catalans 16 =96 43007 Tarragona > Tel +34 977920229 > Fax +34 977920231 > Web: http://www.iciq.es/ > > ________________________________________ >> From: owner-chemistry+wsameera=3D=3Diciq.es_-_ccl.net[owner-chemistry+ws= ameera=3D=3D iciq.es_-_ccl.net] on behalf of Gregorio Garc=EDa Moreno gjgarcia:ujaen.es = [ owner-chemistry_-_ccl.net] > Sent: 22 August 2012 10:13 > To: W.M. Chamil Sameera > Subject: CCL:G: Restart ONIOM optimization from chk file > > Sent to CCL by: =3D?ISO-8859-1?Q?Gregorio_Garc=3DEDa_Moreno?=3D [gjgarcia= ~~ ujaen.es] > Hi > Could I restart an oniom optimization from chk file in Gaussian? How i > do it? > I have tried with opt=3Drestart, but all system (low, medium and high > layers) is placed as high level, i.e. it tries to optimize all system at > the high level. > Thanks in advance > > -- > Gregorio Garc=EDa Morenohttp:// www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_un= sub.shtmlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 --=20 Amir Bernat http://physweb.bgu.ac.il/~bernat/ --20cf300faad5a0502904c7ddf1c5 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Have you added "guess=3Dread"?
I use this on DFT calculations= figured iy should work for you as well, just make sure you keep the origin= al .chk file.

Amir

On Wednesday, August 22, 2012, W.M. Chamil= Sameera wsameera!^!ICIQ.ES <owner-chemistry]=[ccl.net> wrote:
>
> Sent to CCL by: "W.M. Chamil Sameera" [wsameera[a]ICIQ.ES]
> Hi Gregorio,
>
> = Yes, =A0opt=3Drestart can RESTART ONIOM(QM:MM) structure optimization, wher= e Gaussian09 can recover information. Not sure why it does not work for you= .
>
> Simple test: Does Gaussian report ONIOM extrapolated energy at= each optimization step after RESTART?
>
> Sameera.
>
= > .....
> Dr. W. M. C. Sameera
> Institut Catal=E0 d=92Inves= tigaci=F3 Qu=EDmica (ICIQ)
> Av. Pa=EFsos Catalans 16 =96 43007 Tarragona
> Tel +34 977920229=
> Fax +34 977920231
> Web: htt= p://www.iciq.es/
>
> ______________________________________= __
>> From: owner-chemistry+wsameera=3D=3Diciq.es_-_ccl.net [owner-chemistry+wsameera=3D=3Diciq.es_-_ccl.net] on behalf of Gregorio Garc=EDa= Moreno gjgarcia:ujaen.es [owner-chemistry_-_ccl.net]
> Sent: 22 August 2012 10:13
> To: W.M. Chamil Sameera
> Sub= ject: CCL:G: Restart ONIOM optimization from chk file
>
> Sent = to CCL by: =3D?ISO-8859-1?Q?Gregorio_Garc=3DEDa_Moreno?=3D [gjgarcia~~ujaen.es]
> Hi
> Could I restart an oniom optimization from chk file in Gaus= sian? How i
> do it?
> I have tried with opt=3Drestart, but all= system (low, medium and high
> layers) is placed as high level, i.e.= it tries to optimize all system at
> the high level.
> Thanks in advance
>
> --
> G= regorio Garc=EDa Morenohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/c= hemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
>
>
> -=3D This is automatically added to each message by th= e 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.n= et or use:
> =A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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> E-mail to administrators: CHEMISTRY-REQUEST]=[ccl.net or use
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>
> Before posting, check wait time at: http://www.ccl.net
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> Conferences: http://server.ccl.net/chemistry/announcements/confe= rences/
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>
> RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
>
= >
>

--

--=A0
<= /div>


--20cf300faad5a0502904c7ddf1c5-- From owner-chemistry@ccl.net Wed Aug 22 13:56:00 2012 From: "Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= gjgarcia.:.ujaen.es" To: CCL Subject: CCL:G: Restart ONIOM optimization from chk file Message-Id: <-47447-120822135237-25689-i1WUxH4DXlDCu4OZ2H+2kQ]=[server.ccl.net> X-Original-From: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 22 Aug 2012 19:52:28 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= [gjgarcia===ujaen.es] Thanks I will try it from original chk file. Thaks Gregorio > Have you added "guess=read"? > I use this on DFT calculations figured iy should work for you as well, > just > make sure you keep the original .chk file. > > Amir > > On Wednesday, August 22, 2012, W.M. Chamil Sameera wsameera!^!ICIQ.ES < > owner-chemistry]|[ccl.net> wrote: >> >> Sent to CCL by: "W.M. Chamil Sameera" [wsameera[a]ICIQ.ES] >> Hi Gregorio, >> >> Yes, opt=restart can RESTART ONIOM(QM:MM) structure optimization, where > Gaussian09 can recover information. Not sure why it does not work for you. >> >> Simple test: Does Gaussian report ONIOM extrapolated energy at each > optimization step after RESTART? >> >> Sameera. >> >> ..... >> Dr. W. M. C. Sameera >> Institut Català d?Investigació Química (ICIQ) >> Av. Països Catalans 16 ? 43007 Tarragona >> Tel +34 977920229 >> Fax +34 977920231 >> Web: http://www.iciq.es/ >> >> ________________________________________ >>> From: >>> owner-chemistry+wsameera==iciq.es_-_ccl.net[owner-chemistry+wsameera== > iciq.es_-_ccl.net] on behalf of Gregorio García Moreno gjgarcia:ujaen.es [ > owner-chemistry_-_ccl.net] >> Sent: 22 August 2012 10:13 >> To: W.M. Chamil Sameera >> Subject: CCL:G: Restart ONIOM optimization from chk file >> >> Sent to CCL by: Gregorio García Moreno [gjgarcia~~ > ujaen.es] >> Hi >> Could I restart an oniom optimization from chk file in Gaussian? How i >> do it? >> I have tried with opt=restart, but all system (low, medium and high >> layers) is placed as high level, i.e. it tries to optimize all system at >> the high level. >> Thanks in advance >> >> -- >> Gregorio García Morenohttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> >> >> > > -- > > -- > Amir Bernat > http://physweb.bgu.ac.il/~bernat/ > From owner-chemistry@ccl.net Wed Aug 22 16:49:01 2012 From: "Sergio Manzetti sergio.manzetti^-^gmx.com" To: CCL Subject: CCL: Electronnegativity and QM Message-Id: <-47448-120822120911-8550-71PbPOnRvbArXKVTXhle1w*|*server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167021345651737347720" Date: Wed, 22 Aug 2012 18:08:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti-.-gmx.com] --========GMXBoundary167021345651737347720 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear Nikita! Thanks for your clear answer. Is there software to draw this? I am wondering how it can be related to symmetry. Take for instance CCl3, it is tetrahedral with the three chlorine atoms on the "bottom" (If I am not mistaking). How will the electronnegative drawing effect be then? I heard of AIM, however it is not free of charge. Are there free software programs for this? Best wishes Sergio ----- Original Message ----- > From: Nikita Matsunaga Sent: 08/22/12 05:52 PM To: sergio.manzetti**gmx.com Subject: CCL: Electronnegativity and QM Sergio, I just saw your posting on how to see the electronegativity effect using quantum mechanical procedure. Several articles by Ken Wiberg at Yale in mid 80s have exactly what you are talking about. One can follow the "bond path", as defined by Dick Bader in his Atoms in Molecule concept. The bond path between two carbon atoms in ethane, for example, show a straight line. When the bon path is followed for trans-1,2difluroethane, it is curved, and was attributed to electronegativity effect. Nikita ================================================= Nikita Matsunaga Associate Professor Dep. of Chem. & Biochem. Tel (718) 488-1445 Long Island University Fax (718) 488-1465 Brooklyn, NY 11201 Nikita.Matsunaga**liu.edu https://www.gmx.com/callgate-6.60.5.0/rms/6.60.5.0/mail/getBody?folderId=2&messageId=ZXFpb94qRiYoRPt4gW1iz29paNCLO5qD&purpose=display&bodyType=html&reloadHack0.16077347464611091=true# http://myweb.liu.edu/~nmatsuna http://myweb.liu.edu/~nmatsuna&lang=en ================================================= ----- Original Message ----- > From: Nikita Matsunaga Sent: 08/22/12 05:52 PM To: sergio.manzetti**gmx.com Subject: CCL: Electronnegativity and QM --========GMXBoundary167021345651737347720 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

=20 Dear Nikita! Thanks for your clear answer.
=20
=20 Is there software to draw this? I am wondering how it can be related to sy= mmetry. Take for instance CCl3, it is tetrahedral with the three chlorine a= toms on the "bottom" (If I am not mistaking). How will the electronnegative= drawing effect be then?
=20
=20 I heard of AIM, however it is not free of charge. Are there free software = programs for this?
=20
=20 Best wishes
=20
=20
=20 Sergio
=20
=20
=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti**gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =C2=A0

=20
=20
=20
=20
=20
=20 
=20
Sergio,=20

I just saw your posting on how to see the electronegativity effect using qu=
antum mechanical procedure.  Several articles by Ken Wiberg at Yale in mid =
80s have exactly what you are talking about.  One can follow the "bond path=
", as defined by Dick Bader in his Atoms in Molecule concept.  The bond pat=
h between two carbon atoms in ethane, for example, show a straight line.  W=
hen the bon path is followed for trans-1,2difluroethane, it is curved, and =
was attributed to electronegativity effect.=20

Nikita=20


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20

 Nikita Matsunaga            Associate Professor=20

 Dep. of Chem. & Biochem.     Tel (718) 488-1445=20

 Long Island University       Fax (718) 488-1465=20

 Brooklyn, NY 11201     Nikita.Matsunaga**liu.edu<mailto:Nikita.Matsunaga**l=
iu.edu>=20

                  http://myweb.liu=
.edu/~nmatsuna=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
=20
=20

=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti**gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =C2=A0

=20 --========GMXBoundary167021345651737347720-- From owner-chemistry@ccl.net Wed Aug 22 17:24:01 2012 From: "Sergio Manzetti sergio.manzetti{=}gmx.com" To: CCL Subject: CCL: Electronnegativity and QM - correction Message-Id: <-47449-120822121933-9072-2vasMp3RUHLwpnQKvALTKA^server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167031345652366987523" Date: Wed, 22 Aug 2012 18:19:26 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti-x-gmx.com] --========GMXBoundary167031345652366987523 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit I want to correct the former statement, there was an hydrogen missing: HCCl3, it is tetrahedral with the three chlorine atoms on the "bottom" (If I am not mistaking) and hydrogen out of that plane. How will the electronnegative drawing effect be then? I heard of AIM, however it is not free of charge. Are there free software programs for this? Best wishes Sergio ----- Original Message ----- > From: Nikita Matsunaga Sent: 08/22/12 05:52 PM To: sergio.manzetti!=!gmx.com Subject: CCL: Electronnegativity and QM Sergio, I just saw your posting on how to see the electronegativity effect using quantum mechanical procedure. Several articles by Ken Wiberg at Yale in mid 80s have exactly what you are talking about. One can follow the "bond path", as defined by Dick Bader in his Atoms in Molecule concept. The bond path between two carbon atoms in ethane, for example, show a straight line. When the bon path is followed for trans-1,2difluroethane, it is curved, and was attributed to electronegativity effect. Nikita ================================================= Nikita Matsunaga Associate Professor Dep. of Chem. & Biochem. Tel (718) 488-1445 Long Island University Fax (718) 488-1465 Brooklyn, NY 11201 Nikita.Matsunaga!=!liu.edu https://www.gmx.com/callgate-6.60.5.0/rms/6.60.5.0/mail/getBody?folderId=2&messageId=ZXFpb94qRiYoRPt4gW1iz29paNCLO5qD&purpose=display&bodyType=html&reloadHack0.16077347464611091=true# http://myweb.liu.edu/~nmatsuna http://myweb.liu.edu/~nmatsuna&lang=en ================================================= ----- Original Message ----- > From: Nikita Matsunaga Sent: 08/22/12 05:52 PM To: sergio.manzetti!=!gmx.com Subject: CCL: Electronnegativity and QM --========GMXBoundary167031345652366987523 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable
=20

=20 I want= to correct the former statement, there was an hydrogen missing: HCCl3, it = is tetrahedral with the three chlorine atoms on the "bottom" (If I am not m= istaking) and hydrogen out of that plane. How will the electronnegative dra= wing effect be then?
=20
=20 I heard of AIM, however it is not free of charge. Are there free software= programs for this?
=20
=20 Best wishes
=20
=20
=20 Sergio
=20
=20
=20  

=20
=20

=20 ----- Origina= l Message -----

=20

=20 From: Nikita = Matsunaga

=20

=20 Sent: 08/22/1= 2 05:52 PM

=20

=20 To: sergio.ma= nzetti!=!gmx.com

=20

=20 Subject: CCL:= Electronnegativity and QM

=20
=20

=20  =

=20
=20
=20
=20
=20
=20 
=20
=20
Sergio,=20

I just saw your posting on how to see the electronegativity effect using qu=
antum mechanical procedure.  Several articles by Ken Wiberg at Yale in mid =
80s have exactly what you are talking about.  One can follow the "bond path=
", as defined by Dick Bader in his Atoms in Molecule concept.  The bond pat=
h between two carbon atoms in ethane, for example, show a straight line.  W=
hen the bon path is followed for trans-1,2difluroethane, it is curved, and =
was attributed to electronegativity effect.=20

Nikita=20


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20

 Nikita Matsunaga            Associate Professor=20

 Dep. of Chem. & Biochem.     Tel (718) 488-1445=20

 Long Island University       Fax (718) 488-1465=20

 Brooklyn, NY 11201     Nikita.Matsunaga!=!liu.edu<mailto:Nikita.Matsunaga!=!l=
iu.edu>=20

                  http://myweb.liu=
.edu/~nmatsuna=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
=20
=20

=20  =

=20
=20

=20 ----- Origina= l Message -----

=20

=20 From: Nikita = Matsunaga

=20

=20 Sent: 08/22/1= 2 05:52 PM

=20

=20 To: sergio.ma= nzetti!=!gmx.com

=20

=20 Subject: CCL:= Electronnegativity and QM

=20
=20

=20  =

=20
=20 --========GMXBoundary167031345652366987523-- From owner-chemistry@ccl.net Wed Aug 22 22:04:00 2012 From: "ros rodrigogalindo{:}gmail.com" To: CCL Subject: CCL: Electronnegativity and QM Message-Id: <-47450-120822181025-31999-LJgLj/7dwXr1ZdmbYo8ROw###server.ccl.net> X-Original-From: ros Content-Type: multipart/alternative; boundary=e89a8ff1c71e1f36b904c7e20253 Date: Wed, 22 Aug 2012 16:10:18 -0600 MIME-Version: 1.0 Sent to CCL by: ros [rodrigogalindo * gmail.com] --e89a8ff1c71e1f36b904c7e20253 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You can try the excellent program AIMALL by Todd Keith for doing QTAIM. Its free if your system is under 12 atoms. http://aim.tkgristmill.com/ Hope it helps Rodrigo. On Wed, Aug 22, 2012 at 10:08 AM, Sergio Manzetti sergio.manzetti^-^gmx.com wrote: > Dear Nikita! Thanks for your clear answer. > > Is there software to draw this? I am wondering how it can be related to > symmetry. Take for instance CCl3, it is tetrahedral with the three chlori= ne > atoms on the "bottom" (If I am not mistaking). How will the > electronnegative drawing effect be then? > > I heard of AIM, however it is not free of charge. Are there free software > programs for this? > > Best wishes > > > Sergio > > > > > ----- Original Message ----- > > From: Nikita Matsunaga > > Sent: 08/22/12 05:52 PM > > To: sergio.manzetti|-|gmx.com > > Subject: CCL: Electronnegativity and QM > > > > > > > > > Sergio, > > I just saw your posting on how to see the electronegativity effect using = quantum mechanical procedure. Several articles by Ken Wiberg at Yale in mi= d 80s have exactly what you are talking about. One can follow the "bond pa= th", as defined by Dick Bader in his Atoms in Molecule concept. The bond p= ath between two carbon atoms in ethane, for example, show a straight line. = When the bon path is followed for trans-1,2difluroethane, it is curved, an= d was attributed to electronegativity effect. > > Nikita > > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > Nikita Matsunaga Associate Professor > > Dep. of Chem. & Biochem. Tel (718) 488-1445 > > Long Island University Fax (718) 488-1465 > > Brooklyn, NY 11201 Nikita.Matsunaga|-|liu.edu > > > http://myweb.liu.edu/~nmatsuna > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > > ----- Original Message ----- > > From: Nikita Matsunaga > > Sent: 08/22/12 05:52 PM > > To: sergio.manzetti|-|gmx.com > > Subject: CCL: Electronnegativity and QM > > > --e89a8ff1c71e1f36b904c7e20253 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You can try the excellent program AIMALL by Todd Keith for doing QTAIM.=C2= =A0 Its free if your system is under 12 atoms.

http://aim.tkgristmill.com/

Hope it helps
=
Rodrigo.

On Wed, Aug 22, 2012 at 10:08 AM, Sergio Man= zetti sergio.manzetti^-^gmx.com <owne= r-chemistry**ccl.net> wrote:

=20 Dear Nikita! Thanks for your clear answer.
=20
=20 Is there software to draw this? I am wondering how it can be related to sy= mmetry. Take for instance CCl3, it is tetrahedral with the three chlorine a= toms on the "bottom" (If I am not mistaking). How will the electr= onnegative drawing effect be then?
=20
=20 I heard of AIM, however it is not free of charge. Are there free software = programs for this?
=20
=20 Best wishes
=20
=20
=20 Sergio
=20
=20
=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti|-|gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =C2=A0

=20
=20
=20
=20
=20
=20 
=20
Sergio,=20

I just saw your posting on how to see the electronegativity effect using qu=
antum mechanical procedure.  Several articles by Ken Wiberg at Yale in mid =
80s have exactly what you are talking about.  One can follow the "bond=
 path", as defined by Dick Bader in his Atoms in Molecule concept.  Th=
e bond path between two carbon atoms in ethane, for example, show a straigh=
t line.  When the bon path is followed for trans-1,2difluroethane, it is cu=
rved, and was attributed to electronegativity effect.=20

Nikita=20


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20

 Nikita Matsunaga            Associate Professor=20

 Dep. of Chem. & Biochem.     Tel (718) 488-1445=20

 Long Island University       Fax (718) 488-1465=20

 Brooklyn, NY 11201     Nikita.Matsunaga|-|liu.edu<ma=
ilto:Nikita.Matsunaga|-|liu.edu>=20

                  http://myweb.l=
iu.edu/~nmatsuna=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
=20
=20

=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti|-|gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =C2=A0

=20

--e89a8ff1c71e1f36b904c7e20253-- From owner-chemistry@ccl.net Wed Aug 22 22:39:01 2012 From: "Amy Austin amy_jean_austin]![yahoo.com" To: CCL Subject: CCL: Electronnegativity and QM Message-Id: <-47451-120822181721-3561-dd/qhvoo6wlJ+yQz5t5gKw^_^server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="-1192396609-2011384012-1345673834=:9590" Date: Wed, 22 Aug 2012 15:17:14 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin+*+yahoo.com] ---1192396609-2011384012-1345673834=:9590 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =0A=0A=0AGreetings CCLer's,=0A=0AI would like to offer this info in reply t= o Sergio's question:=0A=0A=0AElectronegativity was also addressed in this p= aper by Wiberg:=0A=0A=E2=80=9CIntramolecular nonbonded attractive interacti= ons: 1-substituted =0Apropenes,=E2=80=9D Kenneth B. Wiberg, Yi-gui Wang, Ge= orge A. Petersson, and =0AWilliam F. Bailey, Journal of Chemical Theory and= Computation 5, 1033 (2009)."=0A=0ADispersion is also discussed there. =0A= =0A=0AThe derivation of the dispersion equation reported on this site:=0A= =0Ahttp://gpetersson.faculty.wesleyan.edu/ (See reference [3]) =0A=0A=0Acan= be found in my thesis, published 2008, if anyone is interested in learning= more.=0A=0A=0Ahttp://books.google.com/books/about/Studies_in_Computational= _Quantum_Chemist.html?id=3DrBrWcQAACAAJ=0A=0APlease reply to me privately i= f you would like a copy or to discuss further.=0A=0AAll my best,=0A=0AAmy= =0A=0A=0A=0A=0A=0A________________________________=0A From: Sergio Manzetti= sergio.manzetti^-^gmx.com =0ATo: "Austin, Amy J -= id#4i6-" =0ASent: Wednesday, August 22, 2012 12= :08 PM=0ASubject: CCL: Electronnegativity and QM=0A =0A=0ADear Nikita! Than= ks for your clear answer.=0A=0AIs there software to draw this? I am wonderi= ng how it can be related to symmetry. Take for instance CCl3, it is tetrahe= dral with the three chlorine atoms on the "bottom" (If I am not mistaking).= How will the electronnegative drawing effect be then?=0A=0AI heard of AIM,= however it is not free of charge. Are there free software programs for thi= s?=0A=0ABest wishes=0A=0A=0ASergio=0A=0A=0A=C2=A0=0A----- Original Message = -----=0A>From: Nikita Matsunaga=0A>Sent: 08/22/12 05:52 PM=0A>To: sergio.ma= nzetti|-|gmx.com=0A>Subject: CCL: Electronnegativity and QM=0A=C2=A0=0A=0A= =0A=0A=0A=0ASergio, I just saw your posting on how to see the electronegat= ivity effect using quantum mechanical procedure. Several articles by Ken W= iberg at Yale in mid 80s have exactly what you are talking about. One can = follow the "bond path", as defined by Dick Bader in his Atoms in Molecule c= oncept. The bond path between two carbon atoms in ethane, for example, sho= w a straight line. When the bon path is followed for trans-1,2difluroethan= e, it is curved, and was attributed to electronegativity effect. Nikita = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D N= ikita Matsunaga Associate Professor Dep. of Chem. & Biochem. = Tel (718) 488-1445 Long Island University Fax (718) 488-1465 Broo= klyn, NY 11201 Nikita.Matsunaga|-|liu.edu http://myweb.liu.edu/~nmatsuna&lang=3Den =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =0A=0A=C2=A0=0A----- Original Me= ssage -----=0A>From: Nikita Matsunaga=0A>Sent: 08/22/12 05:52 PM=0A>To: ser= gio.manzetti|-|gmx.com=0A>Subject: CCL: Electronnegativity and QM ---1192396609-2011384012-1345673834=:9590 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable


Greetings CCLer's,

=
I would like to offer this info in reply to Sergio's question:

Electronegativity was a= lso addressed in this paper by Wiberg:

=E2=80=9C= Intramolecular nonbonded attractive interactions: 1-substituted =0Apropenes= ,=E2=80=9D Kenneth B. Wiberg, Yi-gui Wang, George A. Petersson, and =0AWill= iam F. Bailey, Journal of Chemical Theory and Computation 5, 1033 (2009)."

Dispersion is also discusse= d there.

The derivation of the dispersion equ= ation reported on this site:

http://gpetersson.faculty= .wesleyan.edu/ (See reference [3])

can be fou= nd in my thesis, published 2008, if anyone is interested in learning more.<= br>

http://books.google.com/books/about/St= udies_in_Computational_Quantum_Chemist.html?id=3DrBrWcQAACAAJ
Please reply to me privately if you would like a copy or to dis= cuss further.

All my best,

Am= y



= From: Sergio Manzetti sergio.manzet= ti^-^gmx.com <owner-chemistry|*|ccl.net>
To: "Austin, Amy J " <amy_jean_austin|*|yah= oo.com>
Sent: Wedn= esday, August 22, 2012 12:08 PM
S= ubject: CCL: Electronnegativity and QM

= =0A
=0A=09Dear Nikita! Thanks fo= r your clear answer.
=0A=09
=0A=09Is there software to draw this? I= am wondering how it can be related to symmetry. Take for instance CCl3, it= is tetrahedral with the three chlorine atoms on the "bottom" (If I am not = mistaking). How will the electronnegative drawing effect be then?
=0A= =09
=0A=09I heard of AIM, however it is not free of charge. Are there f= ree software programs for this?
=0A=09
=0A=09Best wishes
=0A=09=
=0A=09
=0A=09Sergio
=0A=09
=0A=09
=0A=09 
= =0A
= =0A=09
=0A=09=09----- Original Message --= ---
=0A=09
=0A= =09=09= > From: Nikita Matsunaga
=0A=09
=0A=09=09Sent: 08/22/12 05:52 PM
=0A=09
=0A=09=09To: sergio.manzetti|-|gmx.com
=0A=09
=0A=09=09Subject: CCL: El= ectronnegativity and QM
=0A
=0A
=0A=09 
=0A
=0A
=0A
= =0A
=0A
=0A
 =0ASergio, =0A=0AI just saw your postin=
g on how to see the electronegativity effect using quantum mechanical proce=
dure.  Several articles by Ken Wiberg at Yale in mid 80s have exactly what =
you are talking about.  One can follow the "bond path", as defined by Dick =
Bader in his Atoms in Molecule concept.  The bond path between two carbon a=
toms in ethane, for example, show a straight line.  When the bon path is fo=
llowed for trans-1,2difluroethane, it is curved, and was attributed to elec=
tronegativity effect. =0A=0ANikita =0A=0A=0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =0A=0A Nikita Matsunaga         =
   Associate Professor =0A=0A Dep. of Chem. & Biochem.     Tel (718) 48=
8-1445 =0A=0A Long Island University       Fax (718) 488-1465 =0A=0A Brookl=
yn, NY 11201     Nikita.Matsunaga|-|liu.e=
du<mailto:Nikita.Matsunaga|-|liu.e=
du> =0A=0A                  http://myweb.liu.edu/~nmatsuna&lang=
=3Den =0A=0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D =0A
=0A
=0A
=0A= =09 
=0A
=0A=09
=0A=09=09----- Ori= ginal Message -----
=0A=09
=0A=09=09From: Nikita Matsunaga
=0A=09
=0A=09=09Sent: 08/22/12 05:52 PM =0A=09
=0A=09=09To: sergio.manzetti|-|gm= x.com
=0A=09
=0A= =09=09= Subject: CCL: Electronnegativity and QM
=0A =0A
=0A=09 
=0A<= /span>=0A
<= br>
---1192396609-2011384012-1345673834=:9590-- From owner-chemistry@ccl.net Wed Aug 22 23:14:00 2012 From: "Mark Zottola mzottola]=[gmail.com" To: CCL Subject: CCL: Electronnegativity and QM Message-Id: <-47452-120822184831-13412-1bWQpb8zKvQ2ihZTvsy3JQ(!)server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=e89a8f83aad95ebbd004c7e28add Date: Wed, 22 Aug 2012 18:48:24 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola++gmail.com] --e89a8f83aad95ebbd004c7e28add Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Nikita, In Bader's work on electron density topology and AIM theory, bent bond paths were, in his formalism a measure of pi bonding. I have not seen bond bending as a measure of electronegativity before. Do you have a reference or two from Wiberg? Also, from my understanding of AIM, etc. is that the position of the bond critical point along the bond path is indicative of the relative electronegativity of the two (3,-3) critical points. Can you clarify this for me? Thanks. On Wed, Aug 22, 2012 at 12:08 PM, Sergio Manzetti sergio.manzetti^-^gmx.com wrote: > > ----- Original Message ----- > > From: Nikita Matsunaga > > Sent: 08/22/12 05:52 PM > > To: sergio.manzetti|-|gmx.com > > Subject: CCL: Electronnegativity and QM > > > > > > > > > Sergio, > > I just saw your posting on how to see the electronegativity effect using = quantum mechanical procedure. Several articles by Ken Wiberg at Yale in mi= d 80s have exactly what you are talking about. One can follow the "bond pa= th", as defined by Dick Bader in his Atoms in Molecule concept. The bond p= ath between two carbon atoms in ethane, for example, show a straight line. = When the bon path is followed for trans-1,2difluroethane, it is curved, an= d was attributed to electronegativity effect. > > Nikita > > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > Nikita Matsunaga Associate Professor > > Dep. of Chem. & Biochem. Tel (718) 488-1445 > > Long Island University Fax (718) 488-1465 > > Brooklyn, NY 11201 Nikita.Matsunaga|-|liu.edu > > > http://myweb.liu.edu/~nmatsuna > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > > ----- Original Message ----- > > From: Nikita Matsunaga > > Sent: 08/22/12 05:52 PM > > To: sergio.manzetti|-|gmx.com > > Subject: CCL: Electronnegativity and QM > > > --e89a8f83aad95ebbd004c7e28add Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Nikita,

In Bader's work on electron density topology= and AIM theory, bent bond paths were, in his formalism a measure of pi bon= ding. =A0I have not seen bond bending as a measure of electronegativity bef= ore. =A0Do you have =A0a reference or two from Wiberg?

Also, from my understanding of AIM, etc. is that the po= sition of the bond critical point along the bond path is indicative of the = relative electronegativity of the two (3,-3) critical points. =A0Can you cl= arify this for me?

Thanks.



On Wed, Aug 22, 2012 at 12:08 PM, Sergio Manzetti s= ergio.manzetti^-^gmx.com &= lt;owner-chemi= stry!A!ccl.net> wrote:


=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti|-|gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =A0

=20
=20
=20
=20
=20
=20 
=20
Sergio,=20

I just saw your posting on how to see the electronegativity effect using qu=
antum mechanical procedure.  Several articles by Ken Wiberg at Yale in mid =
80s have exactly what you are talking about.  One can follow the "bond=
 path", as defined by Dick Bader in his Atoms in Molecule concept.  Th=
e bond path between two carbon atoms in ethane, for example, show a straigh=
t line.  When the bon path is followed for trans-1,2difluroethane, it is cu=
rved, and was attributed to electronegativity effect.=20

Nikita=20


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20

 Nikita Matsunaga            Associate Professor=20

 Dep. of Chem. & Biochem.     Tel (718) 488-1445=20

 Long Island University       Fax (718) 488-1465=20

 Brooklyn, NY 11201     Nikita.Matsunaga|-|liu.edu<ma=
ilto:Nikita.Matsunaga|-|liu.edu>=20

                  http://myweb.liu=
.edu/~nmatsuna=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
=20
=20

=20 =A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = Nikita Matsunaga

=20

=20 Sent: = 08/22/12 05:52 PM

=20

=20 To: se= rgio.manzetti|-|gmx.com

=20

=20 Subjec= t: CCL: Electronnegativity and QM

=20
=20

=20 =A0

=20

--e89a8f83aad95ebbd004c7e28add--