From owner-chemistry@ccl.net Sat Apr 30 03:11:00 2011 From: "Sue Lam chsue2004 a yahoo.com" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44499-110430030809-9435-WFClny3615vpaWI5NX71kg_+_server.ccl.net> X-Original-From: Sue Lam Content-Type: multipart/alternative; boundary="0-1778243014-1304147277=:28494" Date: Sat, 30 Apr 2011 00:07:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004**yahoo.com] --0-1778243014-1304147277=:28494 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Servaas, =A0 For the point 2, do you think we could also do the solvent=A0field calculat= ion (single point), on the basis of the gas-phase optimized structure to ge= t the solvent correction? =A0 Sue --- On Fri, 4/29/11, servaas servaas.michielssens**student.kuleuven.be wrote: > From: servaas servaas.michielssens**student.kuleuven.be Subject: CCL:G: implicit solvation To: "L, Sue " Date: Friday, April 29, 2011, 4:08 PM Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] According to the procedure described in Comment on the correct use of continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One should proceed as follows using gaussian 09: 1. Optimize structure in vacuum and do frequency analysis, from this one can find the free energy correction in the gas phase (dGcorr_gas) 2.Optimize the structure in solvent if you are using another solvent model than SMD I think you should add the keyword cav, dis and rep. The energy you get includes all corrections, also the non electrostatic ones. So this it is actually E_solv + Gnes from the above paper. 3. So to find the free energy in solvent one can simply add everything: dGcorr_gas + E_solv + Gnes. I hope that helps, Servaas On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann adieckma[#]googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] > Dear Dave, >=20 > I am aware of that. However, as I understand it frequency calculations sh= ould be done in vacuum as the equations are derived from an ideal gas assum= ption. >=A0 Am I wrong here? And what would be the energy I need to use from the P= CM calculation?=20 >=20 > Cheers, > Arne >=20 > On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: >=20 > >=20 > > Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] > > Arne: > >=A0 You need to do a frequency calculation and then you will have all th= e thermodynamic parameters including the free energy, the zero-point energy= , etc. > >=A0 Regards, Dave Close > >=20 > > -----Original Message----- > >> From: owner-chemistry+closed=3D=3Detsu.edu(!)ccl.net [mailto:owner-che= mistry+closed=3D=3Detsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma= ]_[googlemail.com > > Sent: Thursday, April 28, 2011 8:53 AM > > To: Close, David M. > > Subject: CCL:G: implicit solvation > >=20 > >=20 > > Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] > > Dear all,=20 > >=20 > > I am performing Gaussian calculations using implicit solvation (CPCM). = Afterwards, I would like to apply thermal corrections from gas phase calcul= ations to obtain free energy differences of certain molecules. The Gaussian= output contains several energy values when using implicit solvation, e.g. = "After PCM corrections, the SCF energy is=A0 -193.093761350" and "Total fre= e energy in solution with all non electrostatic terms". Which one would I u= se to add the correction for free energy?=20 > >=20 > >=20 > > Thanks in advance,=20 > > Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/c= hemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>=20 > -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-1778243014-1304147277=:28494 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --0-1778243014-1304147277=:28494--
Hi Servaas,
 
For the point 2, do you think we could also do the solvent field = calculation (single point), on the basis of the gas-phase optimized structu= re to get the solvent correction?
 
Sue


--- On Fri, 4/29/11, servaas servaas.michielssens**s= tudent.kuleuven.be <owner-chemistry^-^ccl.net> wrote:

From: servaas servaas.michielssens**student.kuleu= ven.be <owner-chemistry^-^ccl.net>
Subject: CCL:G: implicit solvatio= n
To: "L, Sue " <chsue2004^-^yahoo.com>
Date: Friday, Apr= il 29, 2011, 4:08 PM


Sent to CCL by: servaas [servaas.michielssens[*]= student.kuleuven.be]
According to the procedure described in Comment on = the correct use of
continuum solvent models (J. Phys. Chem. A 2010, 114,= 13442-13444). One
should proceed as follows using gaussian 09:
1. Op= timize structure in vacuum and do frequency analysis, from this one
can = find the free energy correction in the gas phase (dGcorr_gas)
2.Optimize= the structure in solvent if you are using another solvent
model than SM= D I think you should add the keyword cav, dis and rep. The
energy you ge= t includes all corrections, also the non electrostatic
ones. So this it = is actually E_solv + Gnes from the above paper.
3. So to find the free e= nergy in solvent one can simply add everything:
dGcorr_gas + E_solv + Gn= es.


I hope that helps,

Servaas

On Thu, 2011-04-28 = at 19:53 +0200, Arne Dieckmann
adieckma[#]googlemail.com wrote:
> Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com]<= BR>> Dear Dave,
>
> I am aware of that. However, as I under= stand it frequency calculations should be done in vacuum as the equations a= re derived from an ideal gas assumption.

>  Am I wrong here?= And what would be the energy I need to use from the PCM calculation?
&= gt;
> Cheers,
> Arne
>
> On Apr 28, 2011, at 17:0= 1, "Close, David M. CLOSED^mail.etsu.edu" <owner-chemistry/./ccl.net>= wrote:
>
> >
> > Sent to CCL by: "Close, David M= ." [CLOSED++mail.etsu.edu]
> > Arne:
> >  You need t= o do a frequency calculation and then you will have all the thermodynamic p= arameters including the free energy, the zero-point energy, etc.
> &g= t;  Regards, Dave Close
> >
> > -----Original Messa= ge-----
> >> From: owner-chemistry+closed=3D=3Detsu.edu(!)ccl.net [mailto:owner-chemistry+clo= sed=3D=3Detsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlem= ail.com
> > Sent: Thursday, April 28, 2011 8:53 AM
> > To= : Close, David M.
> > Subject: CCL:G: implicit solvation
> &= gt;
> >
> > Sent to CCL by: "Arne Dieckmann" [adieckma-= --googlemail.com]
> > Dear all,
> >
> > I am p= erforming Gaussian calculations using implicit solvation (CPCM). Afterwards= , I would like to apply thermal corrections from gas phase calculations to = obtain free energy differences of certain molecules. The Gaussian output co= ntains several energy values when using implicit solvation, e.g. "After PCM= corrections, the SCF energy is  -193.093761350" and "Total free energ= y in solution with all non electrostatic terms". Which one would I use to a= dd the correction for free energy?
> >
> >
> >= ; Thanks in advance,
> > Arnehttp://www.ccl.net/cgi-bin/ccl/send_= ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/s= pammers.txt>
>



-=3D This is automatically adde= d to each message by the mailing script =3D-
To recover the email addres= s of the author of the message, please change
the strange characters on = the top line to the ^-^ sign. You can also
look up the X-Original-From: li= ne in the mail header.

E-mail to subscribers: CHEMISTRY^-^ccl.net or use:
      ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administ= rators: CHEMISTRY-REQUEST^-^ccl= .net or use
      http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_message
      http= ://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check w= ait time at: http://www.ccl= .net

Job: ht= tp://www.ccl.net/jobs
Conferences: http://server.ccl.ne= t/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=    =   http://= www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry= /aboutccl/instructions/