From owner-chemistry@ccl.net Sun Jul 3 11:20:01 2016 From: "Andreas Klamt klamt[-]cosmologic.de" To: CCL Subject: CCL:G: Use of solvent in Gaussian-PCM Model Message-Id: <-52274-160703045857-11031-A8j/J+9wtVmfy9LV7yZdKw\a/server.ccl.net> X-Original-From: Andreas Klamt Content-Type: multipart/alternative; boundary="------------7375EEDD73B404F0266A4BB9" Date: Sun, 3 Jul 2016 10:58:45 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] This is a multi-part message in MIME format. --------------7375EEDD73B404F0266A4BB9 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Igor and Rakesh, just a short comment: 1) The results of COSMO or C-PCM are not less accirate as IEFPCM. In a recent paper we demonstrated that both models are essentially indistinguishable, at least if used with correct scaling factor F(eps)=(eps-1)/(eps+.5), which unfortunately is not the default in G09. See: A comprehensive comparison of the IEFPCM and SS (V) PE continuum solvation methods with the COSMO approach A Klamt, C Moya, J Palomar Journal of chemical theory and computation 11 (9), 4220-4225 2) Don't expect that the solvent proproperties of such a strongly hydrogen bonding solvent as triazole will be correctly described by a simple dielectric continuum model. If you want higher accuracy you should try COSMO-RS. Best regards Andreas Am 02.07.2016 um 18:36 schrieb Igors Mihailovs igors.mihailovs0^^gmail.com: > Dear Rakesh Pant, > > Custom solvent can be defined by using additional input section after > the specification of molecule geometry. > In the Route section, SCRF keword will have the following options: > SCRF=(PCM, Solvent=Generic,Read) > while after one blank line below atomic coordinates the following > should appear: > > eps=N.NNN epsinf=M.MMM > > where epsinf is the optical permittivity (refraction index squared). > Note that if you are defining non-equilibrium solvation, corresponding > lines should appear after "eps" lines. > More clear synonym for PCM is IEFPCM which is actually called by > keyword "PCM" in Gaussian 09. In our lab, we usually get rather > qualitative results with CPCM, which has lower computational cost > because of simple model. > > > With best wishes, > Igors Mihailovs (engineer / PhD student) > Institute of Solid State Physics > University of Latvia > > > 2016-07-02 14:57 GMT+03:00 Rakesh Pant rakesh.pant() > students.iiserpune.ac.in > >: > > Dear all, > > I want to use PCM model in Gaussian, and want to know how to use > solvents not listed in Gaussian. > > Suppose I want to use any solvent say triazole or any other > molecule can it done with its dielectric constant ? If yes, then > how can we use any random solvent in PCM model. > > > Thanks > Rakesh > > -- > Rakesh Pant > Research Fellow > IISER Pune, India > Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm > > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt]=[cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt --------------7375EEDD73B404F0266A4BB9 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit
Dear Igor and Rakesh,

just a short comment:
1) The results of COSMO or C-PCM are not less accirate as IEFPCM. In a recent paper we demonstrated that both models are essentially indistinguishable, at least if used with correct scaling factor F(eps)=(eps-1)/(eps+.5), which unfortunately is not the default in G09. See:
A comprehensive comparison of the IEFPCM and SS (V) PE continuum solvation methods with the COSMO approach
A Klamt, C Moya, J Palomar
Journal of chemical theory and computation 11 (9), 4220-4225

2) Don't expect that the solvent proproperties of such a strongly hydrogen bonding solvent as triazole will be correctly described by a simple dielectric continuum model. If you want higher accuracy you should try COSMO-RS.

Best regards

Andreas


Am 02.07.2016 um 18:36 schrieb Igors Mihailovs igors.mihailovs0^^gmail.com:
Dear Rakesh Pant,

Custom solvent can be defined by using additional input section after the specification of molecule geometry.
In the Route section, SCRF keword will have the following options:
SCRF=(PCM, Solvent=Generic,Read)
while after one blank line below atomic coordinates the following should appear:

eps=N.NNN epsinf=M.MMM

where epsinf is the optical permittivity (refraction index squared). Note that if you are defining non-equilibrium solvation, corresponding lines should appear after "eps" lines.
More clear synonym for PCM is IEFPCM which is actually called by keyword "PCM" in Gaussian 09. In our lab, we usually get rather qualitative results with CPCM, which has lower computational cost because of simple model.


With best wishes,
Igors Mihailovs (engineer / PhD student)
Institute of Solid State Physics
University of Latvia


2016-07-02 14:57 GMT+03:00 Rakesh Pant rakesh.pant() students.iiserpune.ac.in <owner-chemistry(_)ccl.net>:
Dear all,

I want to use PCM model in Gaussian, and want to know how to use solvents not listed in Gaussian.

Suppose I want to use any solvent say triazole or any other molecule can it done with its dielectric constant ? If yes, then how can we use any random solvent in PCM model.


Thanks
Rakesh

--
Rakesh Pant
Research Fellow
IISER Pune, India




-- 
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt]=[cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------7375EEDD73B404F0266A4BB9-- From owner-chemistry@ccl.net Sun Jul 3 15:32:00 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor{}fluor.quimica.uniovi.es" To: CCL Subject: CCL: Detecting non-covalent interactions Message-Id: <-52275-160703151843-7983-uhQ/2i1PnZfP2RtelKC9Vw : server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=utf-8 Date: Sun, 03 Jul 2016 21:01:40 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor _ fluor.quimica.uniovi.es] On 2/7/2016 15:41, Henrique C. S. Junior henriquecsj,gmail.com wrote: > Sent to CCL by: "Henrique C. S. Junior" [henriquecsj*gmail.com] > > I’m trying to use nciplot to detect a intermolecular interaction > between two monomers of the type [Cu(II)Cl2(L)2] (L is an inorganic > ligand). The supposed interaction is like this: Henrique, 1) Using an ECP wavefunction requires completing the core electron density appropriately, as the QTAIM analysis must be done on the ED for all electrons. The advise from Sebastian is right in this. 2) Better than nciplot, a preliminary code, you can use a far more advanced version: critic2, distributed freely from the github of the current maintainer: 3) Do not depend on the wfn output from g09. The wfx is better suited for your purpose, and critic2 is able to work with both. From the wfx the program can complete the core density appropriately for the ECP used in your calculation. Good luck and enjoy, Víctor Luaña -- . . "In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion" /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage: Articles: git-hub: From owner-chemistry@ccl.net Sun Jul 3 19:59:01 2016 From: "Henrique C. S. Junior henriquecsj:-:gmail.com" To: CCL Subject: CCL: Detecting non-covalent interactions Message-Id: <-52276-160703185531-25968-0+AbhS9wttQ/mlzuVX9k4Q:_:server.ccl.net> X-Original-From: "Henrique C. S. Junior" Content-Type: multipart/alternative; boundary=001a114080da845a240536c31da4 Date: Sun, 3 Jul 2016 19:54:45 -0300 MIME-Version: 1.0 Sent to CCL by: "Henrique C. S. Junior" [henriquecsj^^gmail.com] --001a114080da845a240536c31da4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear colleagues, thank you all for such detailed answers. I'll give a try to all suggested options. Thank you again. 2016-07-03 16:01 GMT-03:00 V=C3=ADctor Lua=C3=B1a Cabal victor{} fluor.quimica.uniovi.es : > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor _ > fluor.quimica.uniovi.es] > On 2/7/2016 15:41, Henrique C. S. Junior henriquecsj,gmail.com wrote: > > Sent to CCL by: "Henrique C. S. Junior" [henriquecsj*gmail.com] > > > > I=E2=80=99m trying to use nciplot to detect a intermolecular interactio= n > > between two monomers of the type [Cu(II)Cl2(L)2] (L is an inorganic > > ligand). The supposed interaction is like this: > > Henrique, > > 1) Using an ECP wavefunction requires completing the core electron > density appropriately, as the QTAIM analysis must be done on the ED for > all electrons. The advise from Sebastian is right in this. > > 2) Better than nciplot, a preliminary code, you can use a far more > advanced version: critic2, distributed freely from the github of the > current maintainer: > > 3) Do not depend on the wfn output from g09. The wfx is better suited > for your purpose, and critic2 is able to work with both. From the wfx > the program can complete the core density appropriately for the ECP > used in your calculation. > > Good luck and enjoy, > V=C3=ADctor Lua=C3=B1a > > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peo= r > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +--------------------------------------------+ > GroupPage: > Articles: > git-hub: > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Henrique C. S. Junior* Qu=C3=ADmico Industrial - UFRRJ Mestrando em Qu=C3=ADmica Inorg=C3=A2nica - UFRRJ Centro de Processamento de Dados - PMP --001a114080da845a240536c31da4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear colleagues, thank you all for such detailed answers.
I&#= 39;ll give a try to all suggested options.

Thank you again.

2016-07-03 16:= 01 GMT-03:00 V=C3=ADctor Lua=C3=B1a Cabal victor{}fluor.quimica.uniovi.es <owner-chemistry_._ccl.n= et>:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor _ <= a href=3D"http://fluor.quimica.uniovi.es" rel=3D"noreferrer" target=3D"_bla= nk">fluor.quimica.uniovi.es]
=C2=A0On 2/7/2016 15:41, Henrique C. S. Junior henriquecsj,gmail.com wrote:
> Sent to CCL by: "Henrique C. S. Junior" [henriquecsj*gmail.com] >
> I=E2=80=99m trying to use nciplot to detect a intermolecular interacti= on
> between two monomers of the type [Cu(II)Cl2(L)2] (L is an inorganic > ligand). The supposed interaction is like this:

Henrique,

1) Using an ECP wavefunction requires completing the core electron
density appropriately, as the QTAIM analysis must be done on the ED for
all electrons. The advise from Sebastian is right in this.

2) Better than nciplot, a preliminary code, you can use a far more
advanced version: critic2, distributed freely from the github of the
current maintainer: <https://github.com/aoterodelaroza>=

3) Do not depend on the wfn output from g09. The wfx is better suited
for your purpose, and critic2 is able to work with both. From the wfx
the program can complete the core density appropriately for the ECP
used in your calculation.

Good luck and enjoy,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 V=C3= =ADctor Lua=C3=B1a

--
=C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "In science a person can be= convinced by a good argument.
=C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0That is almost impossible in politics = or religion"
=C2=A0 =C2=A0/(o)(o)\=C2=A0 (Adapted from Carl Sagan)
=C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero ta= mbi=C3=A9n es peor
=C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, porque la medio= cridad no es un grado, es una
=C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015=
=C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it i= s also worse than
=C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade,= it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:=C2=A0 <victor#fluor.quimica.uniovi.es>=C2=A0 ! ! phone: +34-985-10= 3491=C2=A0 fax: +34-985-103125 !
+--------------------------------------------+
=C2=A0GroupPage: <http://azufre.quimica.uniovi.es/>
=C2=A0Articles:=C2=A0 <http://= scholar.google.com/citations?user=3DIbl1BWAAAAAJ&hl=3Des>
=C2=A0git-hub:=C2=A0 =C2=A0<https://github.com/aoterodelaroza>



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--
Henriq= ue C. S. Junior
Qu=C3=ADmico Industrial - UFRRJ=
Mestrando em Qu=C3=ADmica Inorg=C3=A2nica - UFRRJCentro de Processamento de Dados - PMP
=
--001a114080da845a240536c31da4--