From owner-chemistry@ccl.net Fri Aug 6 01:23:00 2010
From: "Kalju Kahn kalju(~)chem.ucsb.edu" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: Conformation of trication
Message-Id: <-42457-100805193943-23673-Ms/PdcpmMXkvKWOQtTzA7g^^server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju()chem.ucsb.edu>
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Date: Thu, 5 Aug 2010 16:39:28 -0700
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Sent to CCL by: "Kalju Kahn" [kalju---chem.ucsb.edu]
Hi Vijay:
To add to points mentioned by Thomas and Andreas, keep in mind that
standard minimization will not give you the lowest energy conformer unless
you start with a structure that is structurally similar to the lowest
energy conformer.
You need a conformational search, which does a large number of
minimizations starting with different initial structures. This is
implemented in many molecular mechanics programs (Macromodel in
Schrodinger Suite, SYBYL, TINKER, BOSS ... I would think Discovery Studio
has something like this, too). With 86 atoms you probably do not want to
use ab initio methods, and only a few QM programs offer conformational
search anyways. As Andreas pointed out, you need to treat your solvent.
As a quicker alternative to the rigorous approach he mentioned, one can
specify a dielectric constant. This is a standard option in most
molecular mechanics programs. Keep in mind that "quicker" in
computational chemistry usually translates to "less accurate".
A more rigorous (but also more time-consuming) approach is to set up a
Monte Carlo or Molecular Dynamics simulation (Discovery Studio allows the
latter). You'll still using classical force fields (i.e. not quantum
mechanics) but now with explicit solvent you'll be able to take into
account specific interactions between the solvent ans solute. I am not
sure how the conformations from explicit solvent simulation compare to
COSMO-RS.
Quite frankly, unless the molecule you are looking at is very flexible,
you may have a better luck taking some NMR (E-COSY, NOESY) spectra, and
figuring out the conformation from this data.
Good luck,
Kalju
>
> Sent to CCL by: Andreas Klamt [klamt..cosmologic.de]
> Hi Vijay,
>
> Thomas is basically right, but I think he missed to mention an important
> aspect, i.e. solvation. It is quite unlikely that you are interested in
> your trication in vacuum or gasphase. Most likely you are interested in
> the aqueous solvation. Hence you need to use a combination of a QM with
> a solvation model. Implicit solvation models are most efficient. I am
> convinced that COSMO-RS is most reliable in this regard.
>
> Years ago some Danish people did a comparison on the accuracy of the
> prediction of the right conformers of
> „Conformational analysis of cyclic acidic a-amino acids in aqueous
> solution - an evaluation of different continuum hydration models."
> by Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy
> Liljefors (I am currently not sure whether and where this finally got
> published.)
> Several of the species were ions. COSMO-RS had by far the smallest error
> in this blind prediction test. I am not aware of other method
> comparisons in this regard. Quite surely there are none for triply
> charged species.
>
> Best regards
>
> Andreas
>
>
>
>
> Am 05.08.2010 07:52, schrieb Gkourmpis, Thomas
> Thomas.Gkourmpis[A]borealisgroup.com:
>> Sent to CCL by: "Gkourmpis, Thomas"
>> [Thomas.Gkourmpis---borealisgroup.com]
>> Hi Vijay
>>
>> If the minimum energy configuration is the only thing you're interested
>> in any computational chemistry/physics program will do the job. They all
>> work on similar ways and have routines that do the same things (though
>> in different ways but that's beside the point and does not concern you
>> at this stage). If you use quantum mechanical methods (I assume that's
>> what you're looking for) then the only issues you need to think about is
>> which theory level and basis set will be the best and most efficient way
>> for your particular problem. If you are not interested in electronic
>> properties like wavefunctions, orbitals etc you can always use
>> semiempirical methods that are very fast and relatively accurate.
>> Personally I am using Gaussian, but all other software packages
>> available should be able to perform the energy minimisation task without
>> any problems.
>>
>> I hope this helps
>>
>> Thomas
>>
>>
>> -----Original Message-----
>>
>>> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net
>>> [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net]
>>> On Behalf Of Vijay Tak takvijay(~)gmail.com
>>>
>> Sent: Wednesday, August 04, 2010 7:42 PM
>> To: Gkourmpis, Thomas
>> Subject: CCL: Conformation of trication
>>
>>
>> Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com]
>> Hi CCL,
>> I am very new to computational chemistry. Please help me out.I would
>> like to find the minimum energy conformation of imidazolium based
>> trication ( total 86 atoms).Let me know which software is suitable in
>> this case. Is Discovery studio is appropriate for for this task.
>> Thanks,
>> Vijay Tak
>> takvijay|a|gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>
>>
>>
>>
>
>
> --
> PD. Dr. Andreas Klamt
> CEO / Geschäftsführer
> COSMOlogic GmbH& Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
>
> phone +49-2171-731681
> fax +49-2171-731689
> e-mail klamt!=!cosmologic.de
> web www.cosmologic.de
>
> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH
> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt>
>
>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106
From owner-chemistry@ccl.net Fri Aug 6 01:58:00 2010
From: "Simmie, John john.simmie[#]nuigalway.ie" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42458-100805233032-10199-ukfTVaid+fWGtFGNhdJBCQ-.-server.ccl.net>
X-Original-From: "Simmie, John" <john.simmie-.-nuigalway.ie>
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Date: Fri, 6 Aug 2010 04:25:42 +0100
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Sent to CCL by: "Simmie, John" [john.simmie]-[nuigalway.ie]
This is a multi-part message in MIME format.
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Thomas
You are already calculating the reaction rate at the high-pressure limit
to get the pressue dependent rate constants you need to employ =
RRKM/master
equation theory ... which lies outside the province of Gaussian, Molpro, =
etc
J Simmie::Combustion Chemistry Centre::NUI Galway Ireland
-----Original Message-----
> From: owner-chemistry+john.simmie=3D=3Dnuigalway.ie!=!ccl.net on behalf of =
Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com
Sent: Thu 05/08/2010 14:37
To: Simmie, John
Subject: CCL:G: Reaction Rate as a function of Pressure
=20
Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * =
borealisgroup.com]
Hello everyone
I have a question to ask regarding the pressure and temperature =
dependence on the reaction rate. I am trying to calculate the rate =
constant of a beta scission in a radical (tertbutoxy radical) obtained =
by the decomposition of a peroxide. I am using Gaussian for this job and =
I have no problem in locating the minimum energy configurations for =
products, reactant(s) and transition states. After the final structures =
have been obtained I am running a frequency calculation as a function of =
pressure and temperature to obtain the relevant frequencies, Gibbs Free =
Energies and partition functions I need for the Arrhenius equation.
This is where I have a problem. The frequency outcome as a function of =
temperature is fine and I have no problems with it, but the pressure =
outcome is really puzzling. My results seem to indicate that all the =
thermodynamic quantities that I calculate have almost negligible =
dependence on pressure (especially the frequencies that remain unchanged =
for the same temperature). I am interested in temperature ranges of the =
order 300K-800K and pressures from 1bar to 3000bars. I know from =
experimental data that the reaction constant does change as a function =
of pressure (it gets shifted towards the right as pressure increases), =
but my calculations does not seem to be able to reproduce this =
phenomenon.
One of the reasons I can think about this is the fact that all the =
thermochemical calculations in Gaussian are done under the =
Born-Oppenheimer approximation, but I am not sure if this is the only =
reason (I might be missing something else).
Therefore the favour I want to ask is this: Can anyone tell me if this =
is an effect due only to the approximation I am using? Furthermore if =
this is the case can anybody please suggest any possible ways to apply =
corrections to this approximation for high pressures?
Thanks a lot in advance
Thomas
-=3D This is automatically added to each message by the mailing script =
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From owner-chemistry@ccl.net Fri Aug 6 04:08:00 2010
From: "Gkourmpis, Thomas Thomas.Gkourmpis-,-borealisgroup.com" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42459-100806040621-13286-8HkSkQgTYHIV/8rk8x1ntA(~)server.ccl.net>
X-Original-From: "Gkourmpis, Thomas" <Thomas.Gkourmpis(~)borealisgroup.com>
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Date: Fri, 6 Aug 2010 10:06:07 +0200
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Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com]
Thanks for the answer. I was actually afraid that Gaussian will not be up to the job to get these types of correlations. Are you aware of a software that can perform the RRKM/master equation analysis?
Thanks again
Thomas
-----Original Message-----
> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com^ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com^ccl.net] On Behalf Of Simmie, John john.simmie[#]nuigalway.ie
Sent: Friday, August 06, 2010 5:26 AM
To: Gkourmpis, Thomas
Subject: CCL:G: Reaction Rate as a function of Pressure
Thomas
You are already calculating the reaction rate at the high-pressure limit
to get the pressue dependent rate constants you need to employ RRKM/master
equation theory ... which lies outside the province of Gaussian, Molpro, etc
J Simmie::Combustion Chemistry Centre::NUI Galway Ireland
-----Original Message-----
> From: owner-chemistry+john.simmie==nuigalway.ie-.-ccl.net on behalf of Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com
Sent: Thu 05/08/2010 14:37
To: Simmie, John
Subject: CCL:G: Reaction Rate as a function of Pressure
Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * borealisgroup.com]
Hello everyone
I have a question to ask regarding the pressure and temperature dependence on the reaction rate. I am trying to calculate the rate constant of a beta scission in a radical (tertbutoxy radical) obtained by the decomposition of a peroxide. I am using Gaussian for this job and I have no problem in locating the minimum energy configurations for products, reactant(s) and transition states. After the final structures have been obtained I am running a frequency calculation as a function of pressure and temperature to obtain the relevant frequencies, Gibbs Free Energies and partition functions I need for the Arrhenius equation.
This is where I have a problem. The frequency outcome as a function of temperature is fine and I have no problems with it, but the pressure outcome is really puzzling. My results seem to indicate that all the thermodynamic quantities that I calculate have almost negligible dependence on pressure (especially the frequencies that remain unchanged for the same temperature). I am interested in temperature ranges of the order 300K-800K and pressures from 1bar to 3000bars. I know from experimental data that the reaction constant does change as a function of pressure (it gets shifted towards the right as pressure increases), but my calculations does not seem to be able to reproduce this phenomenon.
One of the reasons I can think about this is the fact that all the thermochemical calculations in Gaussian are done under the Born-Oppenheimer approximation, but I am not sure if this is the only reason (I might be missing something else).
Therefore the favour I want to ask is this: Can anyone tell me if this is an effect due only to the approximation I am using? Furthermore if this is the case can anybody please suggest any possible ways to apply corrections to this approximation for high pressures?
Thanks a lot in advance
Thomashttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D--
-=is is automatically added to each message by the mailing script =http://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 Fri Aug 6 04:42:01 2010
From: "Alain Borel alain.borel,+,epfl.ch" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42460-100806043435-30338-O9+p9lcyjwp4GuSk7vJ/XA-$-server.ccl.net>
X-Original-From: Alain Borel <alain.borel|epfl.ch>
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Date: Fri, 06 Aug 2010 10:34:22 +0200
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Sent to CCL by: Alain Borel [alain.borel]~[epfl.ch]
On 05.08.10 15:37, Thomas Gkourmpis wrote:
> I have a question to ask regarding the pressure and temperature dependence on the reaction rate. I am trying to calculate the rate constant of a beta scission in a radical (tertbutoxy radical) obtained by the decomposition of a peroxide. I am using Gaussian for this job and I have no problem in locating the minimum energy configurations for products, reactant(s) and transition states. After the final structures have been obtained I am running a frequency calculation as a function of pressure and temperature to obtain the relevant frequencies, Gibbs Free Energies and partition functions I need for the Arrhenius equation.
>
> This is where I have a problem. The frequency outcome as a function of temperature is fine and I have no problems with it, but the pressure outcome is really puzzling. My results seem to indicate that all the thermodynamic quantities that I calculate have almost negligible dependence on pressure (especially the frequencies that remain unchanged for the same temperature). I am interested in temperature ranges of the order 300K-800K and pressures from 1bar to 3000bars. I know from experimental data that the reaction constant does change as a function of pressure (it gets shifted towards the right as pressure increases), but my calculations does not seem to be able to reproduce this phenomenon.
How do your calculations model the environment of your system? Pressure
really affects how the molecules of interest interact with the solvent,
for example.
Best regards,
Alain Borel
From owner-chemistry@ccl.net Fri Aug 6 06:09:00 2010
From: "ABHISHEK SHAHI shahi.abhishek1984[A]gmail.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42461-100806060803-25139-l0o1/zYzWwGvVfzY6L4t+Q###server.ccl.net>
X-Original-From: ABHISHEK SHAHI <shahi.abhishek1984 .. gmail.com>
Content-Type: multipart/alternative; boundary=0016367fadb111d113048d24d737
Date: Fri, 6 Aug 2010 15:37:53 +0530
MIME-Version: 1.0
Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984__gmail.com]
--0016367fadb111d113048d24d737
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Hi Thomas
Fortran codes are available for temperature dependence rate constant (TST
theory) and energy dependence rate constant (RRKM theory).But I don't know
any pressure dependence program for rate constant calculation.let me know if
you get something. For RRKM calculation, follow the following LINK. And if
its not helpfull to you then write to auther for Program(free)
ONLINE RRKM CALCULATOR <http://phd.marginean.net/rrkm.html>.
With regards;
ABHISHEK SHAHI
Ph. D. student
Department of Inorganic and Physical Chemistry
IISc bangalore-12
: 080-2293-2384(lab)
Official E-mail: shahi###ipc.iisc.ernet.in
CC: shahi.abhishek1984###gmail.com
On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpis, Thomas Thomas.Gkourmpis-,-
borealisgroup.com <owner-chemistry###ccl.net> wrote:
>
> Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com]
> Thanks for the answer. I was actually afraid that Gaussian will not be up
> to the job to get these types of correlations. Are you aware of a software
> that can perform the RRKM/master equation analysis?
>
> Thanks again
>
> Thomas
>
> -----Original Message-----
> > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com_._ccl.net[mailto:
> owner-chemistry+thomas.gkourmpis <owner-chemistry%2Bthomas.gkourmpis>
> ==borealisgroup.com_._ccl.net] On Behalf Of Simmie, John john.simmie[#]
> nuigalway.ie
> Sent: Friday, August 06, 2010 5:26 AM
> To: Gkourmpis, Thomas
> Subject: CCL:G: Reaction Rate as a function of Pressure
>
> Thomas
> You are already calculating the reaction rate at the high-pressure limit
> to get the pressue dependent rate constants you need to employ RRKM/master
> equation theory ... which lies outside the province of Gaussian, Molpro,
> etc
>
> J Simmie::Combustion Chemistry Centre::NUI Galway Ireland
>
>
> -----Original Message-----
> > From: owner-chemistry+john.simmie==nuigalway.ie-.-ccl.net on behalf of
> Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com
> Sent: Thu 05/08/2010 14:37
> To: Simmie, John
> Subject: CCL:G: Reaction Rate as a function of Pressure
>
>
> Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * borealisgroup.com]
> Hello everyone
>
> I have a question to ask regarding the pressure and temperature dependence
> on the reaction rate. I am trying to calculate the rate constant of a beta
> scission in a radical (tertbutoxy radical) obtained by the decomposition of
> a peroxide. I am using Gaussian for this job and I have no problem in
> locating the minimum energy configurations for products, reactant(s) and
> transition states. After the final structures have been obtained I am
> running a frequency calculation as a function of pressure and temperature to
> obtain the relevant frequencies, Gibbs Free Energies and partition functions
> I need for the Arrhenius equation.
>
> This is where I have a problem. The frequency outcome as a function of
> temperature is fine and I have no problems with it, but the pressure outcome
> is really puzzling. My results seem to indicate that all the thermodynamic
> quantities that I calculate have almost negligible dependence on pressure
> (especially the frequencies that remain unchanged for the same temperature).
> I am interested in temperature ranges of the order 300K-800K and pressures
> from 1bar to 3000bars. I know from experimental data that the reaction
> constant does change as a function of pressure (it gets shifted towards the
> right as pressure increases), but my calculations does not seem to be able
> to reproduce this phenomenon.
>
> One of the reasons I can think about this is the fact that all the
> thermochemical calculations in Gaussian are done under the Born-Oppenheimer
> approximation, but I am not sure if this is the only reason (I might be
> missing something else).
>
> Therefore the favour I want to ask is this: Can anyone tell me if this is
> an effect due only to the approximation I am using? Furthermore if this is
> the case can anybody please suggest any possible ways to apply corrections
> to this approximation for high pressures?
>
> Thanks a lot in advance
>
> Thomashttp://
> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D--
>
>
>
> -=is is automatically added to each message by the mailing script =http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>
>
>
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Content-Transfer-Encoding: quoted-printable
Hi Thomas<br>=A0=A0 Fortran codes are available for temperature dependence =
rate constant (TST theory) and energy dependence rate constant (RRKM theory=
).But I don't know any pressure dependence program for rate constant ca=
lculation.let me know if you get something. For RRKM calculation, follow th=
e following LINK. And if its not helpfull to you then write to auther for P=
rogram(free)<br>
<br><a href=3D"http://phd.marginean.net/rrkm.html">ONLINE RRKM CALCULATOR</=
a>.<br><br><br clear=3D"all">With regards;<br>=A0 ABHISHEK SHAHI <img style=
=3D"margin: 0pt 0.2ex; vertical-align: middle;" src=3D"http://e/softbank_ne=
_jp.7D9"><br>
=A0 Ph. D. student <br>=A0 Department of Inorganic and Physical Chemistry<b=
r>=A0 IISc bangalore-12<br>=A0=A0<img style=3D"margin: 0pt 0.2ex; vertical-=
align: middle;" src=3D"http://e/ezweb_ne_jp.523">:=A0 080-2293-2384(lab)<br=
>=A0 Official E-mail: <a href=3D"mailto:shahi###ipc.iisc.ernet.in" target=3D"=
_blank">shahi###ipc.iisc.ernet.in</a><br>
=A0 CC:=A0 <a href=3D"mailto:shahi.abhishek1984###gmail.com" target=3D"_blank=
">shahi.abhishek1984###gmail.com</a><br>
<br><br><div class=3D"gmail_quote">On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpi=
s, Thomas Thomas.Gkourmpis-,-<a href=3D"http://borealisgroup.com">borealisg=
roup.com</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry###ccl.ne=
t">owner-chemistry###ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . <a href=
=3D"http://borealisgroup.com" target=3D"_blank">borealisgroup.com</a>]<br>
Thanks for the answer. I was actually afraid that Gaussian will not be up t=
o the job to get these types of correlations. Are you aware of a software t=
hat can perform the RRKM/master equation analysis?<br>
<br>
Thanks again<br>
<br>
Thomas<br>
<div class=3D"im"><br>
-----Original Message-----<br>
> From: owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com_._<a hre=
f=3D"http://ccl.net" target=3D"_blank">ccl.net</a> [mailto:<a href=3D"mailt=
o:owner-chemistry%2Bthomas.gkourmpis">owner-chemistry+thomas.gkourmpis</a>=
=3D=3Dborealisgroup.com_._<a href=3D"http://ccl.net" target=3D"_blank">ccl.=
net</a>] On Behalf Of Simmie, John john.simmie[#]<a href=3D"http://nuigalwa=
y.ie" target=3D"_blank">nuigalway.ie</a><br>
Sent: Friday, August 06, 2010 5:26 AM<br>
To: Gkourmpis, Thomas<br>
Subject: CCL:G: Reaction Rate as a function of Pressure<br>
<br>
Thomas<br>
You are already calculating the reaction rate at the high-pressure limit<br=
>
to get the pressue dependent rate constants you need to employ RRKM/master<=
br>
equation theory ... which lies outside the province of Gaussian, Molpro, et=
c<br>
<br>
J Simmie::Combustion Chemistry Centre::NUI Galway Ireland<br>
<br>
<br>
-----Original Message-----<br>
> From: owner-chemistry+john.simmie=3D=3Dnuigalway.ie-.-<a href=3D"http:=
//ccl.net" target=3D"_blank">ccl.net</a> on behalf of Thomas Gkourmpis thom=
as.gkourmpis(~)<a href=3D"http://borealisgroup.com" target=3D"_blank">borea=
lisgroup.com</a><br>
Sent: Thu 05/08/2010 14:37<br>
To: Simmie, John<br>
Subject: CCL:G: Reaction Rate as a function of Pressure<br>
<br>
<br>
Sent to CCL by: "Thomas =A0Gkourmpis" [thomas.gkourmpis * <a href=
=3D"http://borealisgroup.com" target=3D"_blank">borealisgroup.com</a>]<br>
Hello everyone<br>
<br>
</div><div class=3D"im">I have a question to ask regarding the pressure and=
temperature dependence on the reaction rate. I am trying to calculate the =
rate constant of a beta scission in a radical (tertbutoxy radical) obtained=
by the decomposition of a peroxide. I am using Gaussian for this job and I=
have no problem in locating the minimum energy configurations for products=
, reactant(s) and transition states. After the final structures have been o=
btained I am running a frequency calculation as a function of pressure and =
temperature to obtain the relevant frequencies, Gibbs Free Energies and par=
tition functions I need for the Arrhenius equation.<br>
<br>
This is where I have a problem. The frequency outcome as a function of temp=
erature is fine and I have no problems with it, but the pressure outcome is=
really puzzling. My results seem to indicate that all the thermodynamic qu=
antities that I calculate have almost negligible dependence on pressure (es=
pecially the frequencies that remain unchanged for the same temperature). I=
am interested in temperature ranges of the order 300K-800K and pressures f=
rom 1bar to 3000bars. I know from experimental data that the reaction const=
ant does change as a function of pressure (it gets shifted towards the righ=
t as pressure increases), but my calculations does not seem to be able to r=
eproduce this phenomenon.<br>
<br>
</div><div class=3D"im">One of the reasons I can think about this is the fa=
ct that all the thermochemical calculations in Gaussian are done under the =
Born-Oppenheimer approximation, but I am not sure if this is the only reaso=
n (I might be missing something else).<br>
<br>
Therefore the favour I want to ask is this: Can anyone tell me if this is a=
n effect due only to the approximation I am using? Furthermore if this is t=
he case can anybody please suggest any possible ways to apply corrections t=
o this approximation for high pressures?<br>
<br>
Thanks a lot in advance<br>
<br>
</div>Thomashttp://<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_messa=
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--0016367fadb111d113048d24d737--
From owner-chemistry@ccl.net Fri Aug 6 07:56:00 2010
From: "Gkourmpis, Thomas Thomas.Gkourmpis[-]borealisgroup.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42462-100806075418-15780-I7rmrCuHlO0Y8xZVHakJzg]_[server.ccl.net>
X-Original-From: "Gkourmpis, Thomas" <Thomas.Gkourmpis%x%borealisgroup.com>
Content-Language: en-US
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boundary="_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_"
Date: Fri, 6 Aug 2010 13:53:00 +0200
MIME-Version: 1.0
Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis:_:borealisgroup.com]
--_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_
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Thanks a lot for all the answers guys=2E They're most appreciated=2E I will=
look for the relevant software you recommended and I will also check the l=
iterature on the subject again to see what I can dig up=2E=0D=0A=0D=0AAlain=
the calculations that I have done so far are in the gas phase, and I am do=
ing them in a solvent as we speak=2E I can imagine that the solvent will be=
heavily affected by the pressure, but I was expecting to see some effect (=
a bit smaller but still measurable) in the gas as well=2E=0D=0A=0D=0AAgain =
thanks a lot=0D=0A=0D=0AThomas=0D=0A=0D=0A=0D=0AFrom: owner-chemistry+thoma=
s=2Egkourmpis=3D=3Dborealisgroup=2Ecom]^[ccl=2Enet [mailto:owner-chemistry+th=
omas=2Egkourmpis=3D=3Dborealisgroup=2Ecom]^[ccl=2Enet] On Behalf Of ABHISHEK =
SHAHI shahi=2Eabhishek1984[A]gmail=2Ecom=0D=0ASent: Friday, August 06, 2010=
12:08 PM=0D=0ATo: Gkourmpis, Thomas=0D=0ASubject: CCL:G: Reaction Rate as =
a function of Pressure=0D=0A=0D=0AHi Thomas=0D=0A Fortran codes are avail=
able for temperature dependence rate constant (TST theory) and energy depen=
dence rate constant (RRKM theory)=2EBut I don't know any pressure dependenc=
e program for rate constant calculation=2Elet me know if you get something=
=2E For RRKM calculation, follow the following LINK=2E And if its not helpf=
ull to you then write to auther for Program(free)=0D=0A=0D=0AONLINE RRKM CA=
LCULATOR<http://phd=2Emarginean=2Enet/rrkm=2Ehtml>=2E=0D=0A=0D=0A=0D=0AWith=
regards;=0D=0A ABHISHEK SHAHI [http://e/softbank_ne_jp=2E7D9]=0D=0A Ph=
=2E D=2E student=0D=0A Department of Inorganic and Physical Chemistry=0D=
=0A IISc bangalore-12=0D=0A [http://e/ezweb_ne_jp=2E523] : 080-2293-2384=
(lab)=0D=0A Official E-mail: shahi() ipc=2Eiisc=2Eernet=2Ein<mailto:shahi(=
)%20ipc=2Eiisc=2Eernet=2Ein>=0D=0A CC: shahi=2Eabhishek1984() gmail=2Ecom=
<mailto:shahi=2Eabhishek1984()%20gmail=2Ecom>=0D=0A=0D=0AOn Fri, Aug 6, 201=
0 at 1:36 PM, Gkourmpis, Thomas Thomas=2EGkourmpis-,-borealisgroup=2Ecom<ht=
tp://borealisgroup=2Ecom> <owner-chemistry() ccl=2Enet<mailto:owner-chemist=
ry()%20ccl=2Enet>> wrote:=0D=0A=0D=0ASent to CCL by: "Gkourmpis, Thomas" [T=
homas=2EGkourmpis =2E borealisgroup=2Ecom<http://borealisgroup=2Ecom>]=0D=
=0AThanks for the answer=2E I was actually afraid that Gaussian will not be=
up to the job to get these types of correlations=2E Are you aware of a sof=
tware that can perform the RRKM/master equation analysis?=0D=0A=0D=0AThanks=
again=0D=0A=0D=0AThomas=0D=0A=0D=0A-----Original Message-----=0D=0A> From:=
owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom_=2E_ccl=2Enet<=
http://ccl=2Enet> [mailto:owner-chemistry+thomas=2Egkourmpis<mailto:owner-c=
hemistry%2Bthomas=2Egkourmpis>=3D=3Dborealisgroup=2Ecom_=2E_ccl=2Enet<http:=
//ccl=2Enet>] On Behalf Of Simmie, John john=2Esimmie[#]nuigalway=2Eie<http=
://nuigalway=2Eie>=0D=0ASent: Friday, August 06, 2010 5:26 AM=0D=0ATo: Gkou=
rmpis, Thomas=0D=0ASubject: CCL:G: Reaction Rate as a function of Pressure=
=0D=0A=0D=0AThomas=0D=0AYou are already calculating the reaction rate at th=
e high-pressure limit=0D=0Ato get the pressue dependent rate constants you =
need to employ RRKM/master=0D=0Aequation theory =2E=2E=2E which lies outsid=
e the province of Gaussian, Molpro, etc=0D=0A=0D=0AJ Simmie::Combustion Che=
mistry Centre::NUI Galway Ireland=0D=0A=0D=0A=0D=0A-----Original Message---=
--=0D=0A> From: owner-chemistry+john=2Esimmie=3D=3Dnuigalway=2Eie-=2E-ccl=
=2Enet<http://ccl=2Enet> on behalf of Thomas Gkourmpis thomas=2Egkourmpis(~=
)borealisgroup=2Ecom<http://borealisgroup=2Ecom>=0D=0ASent: Thu 05/08/2010 =
14:37=0D=0ATo: Simmie, John=0D=0ASubject: CCL:G: Reaction Rate as a functio=
n of Pressure=0D=0A=0D=0A=0D=0ASent to CCL by: "Thomas Gkourmpis" [thomas=
=2Egkourmpis * borealisgroup=2Ecom<http://borealisgroup=2Ecom>]=0D=0AHello =
everyone=0D=0AI have a question to ask regarding the pressure and temperatu=
re dependence on the reaction rate=2E I am trying to calculate the rate con=
stant of a beta scission in a radical (tertbutoxy radical) obtained by the =
decomposition of a peroxide=2E I am using Gaussian for this job and I have =
no problem in locating the minimum energy configurations for products, reac=
tant(s) and transition states=2E After the final structures have been obtai=
ned I am running a frequency calculation as a function of pressure and temp=
erature to obtain the relevant frequencies, Gibbs Free Energies and partiti=
on functions I need for the Arrhenius equation=2E=0D=0A=0D=0AThis is where =
I have a problem=2E The frequency outcome as a function of temperature is f=
ine and I have no problems with it, but the pressure outcome is really puzz=
ling=2E My results seem to indicate that all the thermodynamic quantities t=
hat I calculate have almost negligible dependence on pressure (especially t=
he frequencies that remain unchanged for the same temperature)=2E I am inte=
rested in temperature ranges of the order 300K-800K and pressures from 1bar=
to 3000bars=2E I know from experimental data that the reaction constant do=
es change as a function of pressure (it gets shifted towards the right as p=
ressure increases), but my calculations does not seem to be able to reprodu=
ce this phenomenon=2E=0D=0AOne of the reasons I can think about this is the=
fact that all the thermochemical calculations in Gaussian are done under t=
he Born-Oppenheimer approximation, but I am not sure if this is the only re=
ason (I might be missing something else)=2E=0D=0A=0D=0ATherefore the favour=
I want to ask is this: Can anyone tell me if this is an effect due only to=
the approximation I am using? Furthermore if this is the case can anybody =
please suggest any possible ways to apply corrections to this approximation=
for high pressures?=0D=0A=0D=0AThanks a lot in advance=0D=0AThomashttp://w=
ww=2Eccl=2Enet/cgi-bin/ccl/send_ccl_messagehttp://www=2Eccl=2Enet/spammers=
=2Etxt------_=3DextPart_001_01CB3517=2EB44B3B5D--<http://www=2Eccl=2Enet/cg=
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--_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_
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85pt;}=0D=0Adiv=2EWordSection1=0D=0A {page:WordSection1;}=0D=0A-->=0D=0A</s=
tyle>=0D=0A<!--[if gte mso 9]><xml>=0D=0A <o:shapedefaults v:ext=3D"edit" s=
pidmax=3D"1026" />=0D=0A</xml><![endif]--><!--[if gte mso 9]><xml>=0D=0A <o=
:shapelayout v:ext=3D"edit">=0D=0A <o:idmap v:ext=3D"edit" data=3D"1" />=
=0D=0A </o:shapelayout></xml><![endif]-->=0D=0A</head>=0D=0A=0D=0A<body lan=
g=3DEN-GB link=3Dblue vlink=3Dpurple>=0D=0A=0D=0A<div class=3DWordSection1>=
=0D=0A=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-fam=
ily:"Arial","sans-serif";=0D=0Acolor:#1F497D'>Thanks a lot for all the answ=
ers guys=2E They’re most=0D=0Aappreciated=2E I will look for the rele=
vant software you recommended and I will=0D=0Aalso check the literature on =
the subject again to see what I can dig up=2E<o:p></o:p></span></p>=0D=0A=
=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-family:"A=
rial","sans-serif";=0D=0Acolor:#1F497D'><o:p> </o:p></span></p>=0D=0A=
=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-family:"A=
rial","sans-serif";=0D=0Acolor:#1F497D'>Alain the calculations that I have =
done so far are in the gas=0D=0Aphase, and I am doing them in a solvent as =
we speak=2E I can imagine that the=0D=0Asolvent will be heavily affected by=
the pressure, but I was expecting to see=0D=0Asome effect (a bit smaller b=
ut still measurable) in the gas as well=2E<o:p></o:p></span></p>=0D=0A=0D=
=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-family:"Aria=
l","sans-serif";=0D=0Acolor:#1F497D'><o:p> </o:p></span></p>=0D=0A=0D=
=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-family:"Aria=
l","sans-serif";=0D=0Acolor:#1F497D'>Again thanks a lot<o:p></o:p></span></=
p>=0D=0A=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-f=
amily:"Arial","sans-serif";=0D=0Acolor:#1F497D'><o:p> </o:p></span></p=
>=0D=0A=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-fa=
mily:"Arial","sans-serif";=0D=0Acolor:#1F497D'>Thomas<o:p></o:p></span></p>=
=0D=0A=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-fam=
ily:"Arial","sans-serif";=0D=0Acolor:#1F497D'><o:p> </o:p></span></p>=
=0D=0A=0D=0A<p class=3DMsoNormal><span style=3D'font-size:10=2E0pt;font-fam=
ily:"Arial","sans-serif";=0D=0Acolor:#1F497D'><o:p> </o:p></span></p>=
=0D=0A=0D=0A<div style=3D'border:none;border-top:solid #B5C4DF 1=2E0pt;padd=
ing:3=2E0pt 0cm 0cm 0cm'>=0D=0A=0D=0A<p class=3DMsoNormal><b><span lang=3DE=
N-US style=3D'font-size:10=2E0pt;font-family:=0D=0A"Tahoma","sans-serif"'>F=
rom:</span></b><span lang=3DEN-US style=3D'font-size:10=2E0pt;=0D=0Afont-fa=
mily:"Tahoma","sans-serif"'>=0D=0Aowner-chemistry+thomas=2Egkourmpis=3D=3Db=
orealisgroup=2Ecom]^[ccl=2Enet=0D=0A[mailto:owner-chemistry+thomas=2Egkourmpi=
s=3D=3Dborealisgroup=2Ecom]^[ccl=2Enet] <b>On=0D=0ABehalf Of </b>ABHISHEK SHA=
HI shahi=2Eabhishek1984[A]gmail=2Ecom<br>=0D=0A<b>Sent:</b> Friday, August =
06, 2010 12:08 PM<br>=0D=0A<b>To:</b> Gkourmpis, Thomas<br>=0D=0A<b>Subject=
:</b> CCL:G: Reaction Rate as a function of Pressure<o:p></o:p></span></p>=
=0D=0A=0D=0A</div>=0D=0A=0D=0A<p class=3DMsoNormal><o:p> </o:p></p>=0D=
=0A=0D=0A<p class=3DMsoNormal style=3D'margin-bottom:12=2E0pt'>Hi Thomas<br=
>=0D=0A Fortran codes are available for temperature dependence =
rate=0D=0Aconstant (TST theory) and energy dependence rate constant (RRKM t=
heory)=2EBut I=0D=0Adon't know any pressure dependence program for rate con=
stant calculation=2Elet me=0D=0Aknow if you get something=2E For RRKM calcu=
lation, follow the following LINK=2E And=0D=0Aif its not helpfull to you th=
en write to auther for Program(free)<br>=0D=0A<br>=0D=0A<a href=3D"http://p=
hd=2Emarginean=2Enet/rrkm=2Ehtml">ONLINE RRKM CALCULATOR</a>=2E<br>=0D=0A<b=
r>=0D=0A<br clear=3Dall>=0D=0AWith regards;<br>=0D=0A ABHISHEK SHAHI =
<img border=3D0 id=3D"_x0000_i1025"=0D=0Asrc=3D"http://e/softbank_ne_jp=2E7=
D9"><br>=0D=0A Ph=2E D=2E student <br>=0D=0A Department of Inor=
ganic and Physical Chemistry<br>=0D=0A IISc bangalore-12<br>=0D=0A&nb=
sp; <img border=3D0 id=3D"_x0000_i1026" src=3D"http://e/ezweb_ne_jp=2E=
523">: =0D=0A080-2293-2384(lab)<br>=0D=0A Official E-mail: <a hr=
ef=3D"mailto:shahi()%20ipc=2Eiisc=2Eernet=2Ein"=0D=0Atarget=3D"_blank">shah=
i() ipc=2Eiisc=2Eernet=2Ein</a><br>=0D=0A CC: <a href=3D"mailto=
:shahi=2Eabhishek1984()%20gmail=2Ecom"=0D=0Atarget=3D"_blank">shahi=2Eabhis=
hek1984() gmail=2Ecom</a><br>=0D=0A<br>=0D=0A<o:p></o:p></p>=0D=0A=0D=0A<di=
v>=0D=0A=0D=0A<p class=3DMsoNormal>On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpi=
s, Thomas=0D=0AThomas=2EGkourmpis-,-<a href=3D"http://borealisgroup=2Ecom">=
borealisgroup=2Ecom</a>=0D=0A<<a href=3D"mailto:owner-chemistry()%20ccl=
=2Enet">owner-chemistry() ccl=2Enet</a>>=0D=0Awrote:<o:p></o:p></p>=0D=
=0A=0D=0A<p class=3DMsoNormal><br>=0D=0ASent to CCL by: "Gkourmpis, Th=
omas" [Thomas=2EGkourmpis =2E <a=0D=0Ahref=3D"http://borealisgroup=2Ec=
om" target=3D"_blank">borealisgroup=2Ecom</a>]<br>=0D=0AThanks for the answ=
er=2E I was actually afraid that Gaussian will not be up to=0D=0Athe job to=
get these types of correlations=2E Are you aware of a software that=0D=0Ac=
an perform the RRKM/master equation analysis?<br>=0D=0A<br>=0D=0AThanks aga=
in<br>=0D=0A<br>=0D=0AThomas<o:p></o:p></p>=0D=0A=0D=0A<div>=0D=0A=0D=0A<p =
class=3DMsoNormal style=3D'margin-bottom:12=2E0pt'><br>=0D=0A-----Original =
Message-----<br>=0D=0A> From: owner-chemistry+thomas=2Egkourmpis=3D=3Dbo=
realisgroup=2Ecom_=2E_<a=0D=0Ahref=3D"http://ccl=2Enet" target=3D"_blank">c=
cl=2Enet</a> [mailto:<a=0D=0Ahref=3D"mailto:owner-chemistry%2Bthomas=2Egkou=
rmpis">owner-chemistry+thomas=2Egkourmpis</a>=3D=3Dborealisgroup=2Ecom_=2E_=
<a=0D=0Ahref=3D"http://ccl=2Enet" target=3D"_blank">ccl=2Enet</a>] On Behal=
f Of Simmie, John=0D=0Ajohn=2Esimmie[#]<a href=3D"http://nuigalway=2Eie" ta=
rget=3D"_blank">nuigalway=2Eie</a><br>=0D=0ASent: Friday, August 06, 2010 5=
:26 AM<br>=0D=0ATo: Gkourmpis, Thomas<br>=0D=0ASubject: CCL:G: Reaction Rat=
e as a function of Pressure<br>=0D=0A<br>=0D=0AThomas<br>=0D=0AYou are alre=
ady calculating the reaction rate at the high-pressure limit<br>=0D=0Ato ge=
t the pressue dependent rate constants you need to employ RRKM/master<br>=
=0D=0Aequation theory =2E=2E=2E which lies outside the province of Gaussian=
, Molpro, etc<br>=0D=0A<br>=0D=0AJ Simmie::Combustion Chemistry Centre::NUI=
Galway Ireland<br>=0D=0A<br>=0D=0A<br>=0D=0A-----Original Message-----<br>=
=0D=0A> From: owner-chemistry+john=2Esimmie=3D=3Dnuigalway=2Eie-=2E-<a h=
ref=3D"http://ccl=2Enet"=0D=0Atarget=3D"_blank">ccl=2Enet</a> on behalf of =
Thomas Gkourmpis thomas=2Egkourmpis(~)<a=0D=0Ahref=3D"http://borealisgroup=
=2Ecom" target=3D"_blank">borealisgroup=2Ecom</a><br>=0D=0ASent: Thu 05/08/=
2010 14:37<br>=0D=0ATo: Simmie, John<br>=0D=0ASubject: CCL:G: Reaction Rate=
as a function of Pressure<br>=0D=0A<br>=0D=0A<br>=0D=0ASent to CCL by: &qu=
ot;Thomas Gkourmpis" [thomas=2Egkourmpis * <a=0D=0Ahref=3D"http:=
//borealisgroup=2Ecom" target=3D"_blank">borealisgroup=2Ecom</a>]<br>=0D=0A=
Hello everyone<o:p></o:p></p>=0D=0A=0D=0A</div>=0D=0A=0D=0A<div>=0D=0A=0D=
=0A<p class=3DMsoNormal style=3D'margin-bottom:12=2E0pt'>I have a question =
to ask=0D=0Aregarding the pressure and temperature dependence on the reacti=
on rate=2E I am=0D=0Atrying to calculate the rate constant of a beta scissi=
on in a radical=0D=0A(tertbutoxy radical) obtained by the decomposition of =
a peroxide=2E I am using=0D=0AGaussian for this job and I have no problem i=
n locating the minimum energy=0D=0Aconfigurations for products, reactant(s)=
and transition states=2E After the final=0D=0Astructures have been obtaine=
d I am running a frequency calculation as a=0D=0Afunction of pressure and t=
emperature to obtain the relevant frequencies, Gibbs=0D=0AFree Energies and=
partition functions I need for the Arrhenius equation=2E<br>=0D=0A<br>=0D=
=0AThis is where I have a problem=2E The frequency outcome as a function of=
=0D=0Atemperature is fine and I have no problems with it, but the pressure =
outcome is=0D=0Areally puzzling=2E My results seem to indicate that all the=
thermodynamic=0D=0Aquantities that I calculate have almost negligible depe=
ndence on pressure=0D=0A(especially the frequencies that remain unchanged f=
or the same temperature)=2E I=0D=0Aam interested in temperature ranges of t=
he order 300K-800K and pressures from=0D=0A1bar to 3000bars=2E I know from =
experimental data that the reaction constant does=0D=0Achange as a function=
of pressure (it gets shifted towards the right as pressure=0D=0Aincreases)=
, but my calculations does not seem to be able to reproduce this=0D=0Apheno=
menon=2E<o:p></o:p></p>=0D=0A=0D=0A</div>=0D=0A=0D=0A<div>=0D=0A=0D=0A<p cl=
ass=3DMsoNormal style=3D'margin-bottom:12=2E0pt'>One of the reasons I can t=
hink=0D=0Aabout this is the fact that all the thermochemical calculations i=
n Gaussian are=0D=0Adone under the Born-Oppenheimer approximation, but I am=
not sure if this is the=0D=0Aonly reason (I might be missing something els=
e)=2E<br>=0D=0A<br>=0D=0ATherefore the favour I want to ask is this: Can an=
yone tell me if this is an=0D=0Aeffect due only to the approximation I am u=
sing? Furthermore if this is the=0D=0Acase can anybody please suggest any p=
ossible ways to apply corrections to this=0D=0Aapproximation for high press=
ures?<br>=0D=0A<br>=0D=0AThanks a lot in advance<o:p></o:p></p>=0D=0A=0D=0A=
</div>=0D=0A=0D=0A<p class=3DMsoNormal>Thomashttp://<a=0D=0Ahref=3D"http://=
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--_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_--
From owner-chemistry@ccl.net Fri Aug 6 10:41:01 2010
From: "William Flak williamflak++yahoo.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42463-100806103711-6512-BZ2PDxfzDubKuc1+M4m0qQ++server.ccl.net>
X-Original-From: "William Flak" <williamflak|a|yahoo.com>
Date: Fri, 6 Aug 2010 10:37:10 -0400
Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
Dear CCL users
This may be a trivial question, I am not a student but I got confused and my
colleagues here say different answers.
For A + B ---> C, comparing the Gibbs free energy for this reaction by:
G(a)= H(a) - TS
G(b)= H(b) - TS
G(c)= H(c) - TS
What is the correct way to calculate G (reaction)?
G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated jobs
or
G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job and
separated from each other by 50A
These two methods are different and giving different results at the same level
of calculation. Counting TS twice in the first equation may be a reason, but in
the second equation accounting rotation and transition degrees is also a
problem.
Is there another equation you use?
Any kind of help would be appreciated
Thanks in advance
Flak
From owner-chemistry@ccl.net Fri Aug 6 11:40:01 2010
From: "Charles Johnson cjohns98^-^slu.edu" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42464-100806113831-14971-kukm6KBEKmjJfHwEeDEoig[a]server.ccl.net>
X-Original-From: Charles Johnson <cjohns98|slu.edu>
Content-Type: multipart/alternative; boundary=001517503b22e4790a048d297481
Date: Fri, 6 Aug 2010 10:38:21 -0500
MIME-Version: 1.0
Sent to CCL by: Charles Johnson [cjohns98]^[slu.edu]
--001517503b22e4790a048d297481
Content-Type: text/plain; charset=ISO-8859-1
I would first calculate G for each, A, B and C individually. Then use the
equation G(rxn)=G(c)-(G(a)+G(b)).
hope that helps
On Fri, Aug 6, 2010 at 9:37 AM, William Flak williamflak++yahoo.com <
owner-chemistry[-]ccl.net> wrote:
>
> Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
> Dear CCL users
> This may be a trivial question, I am not a student but I got confused and
> my
> colleagues here say different answers.
> For A + B ---> C, comparing the Gibbs free energy for this reaction by:
> G(a)= H(a) - TS
> G(b)= H(b) - TS
> G(c)= H(c) - TS
>
> What is the correct way to calculate G (reaction)?
> G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated jobs
> or
> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job
> and
> separated from each other by 50A
>
> These two methods are different and giving different results at the same
> level
> of calculation. Counting TS twice in the first equation may be a reason,
> but in
> the second equation accounting rotation and transition degrees is also a
> problem.
> Is there another equation you use?
> Any kind of help would be appreciated
> Thanks in advance
> Flak>
>
>
--
Charles A. Johnson
Graduate Student
Department of Chemistry
--001517503b22e4790a048d297481
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
I would first calculate G for each, A, B and C individually.=A0 Then use th=
e equation G(rxn)=3DG(c)-(G(a)+G(b)).<br><br>hope that helps<br><br><div cl=
ass=3D"gmail_quote">On Fri, Aug 6, 2010 at 9:37 AM, William Flak williamfla=
k++<a href=3D"http://yahoo.com">yahoo.com</a> <span dir=3D"ltr"><<a href=
=3D"mailto:owner-chemistry[-]ccl.net">owner-chemistry[-]ccl.net</a>></span> =
wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: "William =A0Flak" [williamflak^^<a href=3D"http:/=
/yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Dear CCL users<br>
This may be a trivial question, I am not a student but I got confused and m=
y<br>
colleagues here say different answers.<br>
For A + B ---> C, comparing the Gibbs free energy for this reaction by:<=
br>
G(a)=3D H(a) - TS<br>
G(b)=3D H(b) - TS<br>
G(c)=3D H(c) - TS<br>
<br>
What is the correct way to calculate G (reaction)?<br>
=A0G(reaction) =3D G(c) - G(a) - G(b) here A and B calculated in separated =
jobs<br>
or<br>
=A0G(reaction) =3D G(c) - G((a)&(b)) here A and B calculated in one sin=
gle job and<br>
separated from each other by 50A<br>
<br>
These two methods are different and giving different results at the same le=
vel<br>
of calculation. Counting TS twice in the first equation may be a reason, bu=
t in<br>
the second equation accounting rotation and transition degrees is also a<br=
>
problem.<br>
Is there another equation you use?<br>
Any kind of help would be appreciated<br>
Thanks in advance<br>
Flak<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
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nferences/</a><br>
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=A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
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<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Charles A. Johnson<br>G=
raduate Student<br>Department of Chemistry<br><br><br>
--001517503b22e4790a048d297481--
From owner-chemistry@ccl.net Fri Aug 6 14:19:01 2010
From: "Ol Ga eurisco1!=!pochta.ru" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42465-100806114751-26959-pXwTA1xFmJmvqTtzrZMdbQ(!)server.ccl.net>
X-Original-From: "Ol Ga" <eurisco1]*[pochta.ru>
Date: Fri, 6 Aug 2010 11:47:50 -0400
Sent to CCL by: "Ol Ga" [eurisco1 .. pochta.ru]
Dear William Flak,
First of all we should answer how to calculate energy of this reaction. If the QC method is not size-consistent (e.g., available DFT functionals), the second strategy defined by your words
> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job and > separated from each other by 50A
is completely wrong. In this case it is necessary to make 3 separate calculations.
If the QC method is size-consistent, in principle it is possible to apply both strategies. I would note that 50 A is too crude, maybe 7-10 A is more convenient.
About entropy of the reaction: really it is difficult to calculate with high precision.
Sincerely,
Ol Ga
--------------------------------------------------
> From: "William Flak williamflak++yahoo.com" <owner-chemistry[*]ccl.net>
Sent: Friday, August 06, 2010 6:37 PM
To: "Ga, Ol " <eurisco1[*]pochta.ru>
Subject: CCL: Gibbs free energy
>
>
> Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
> Dear CCL users
> This may be a trivial question, I am not a student but I got confused and my
> colleagues here say different answers.
> For A + B ---> C, comparing the Gibbs free energy for this reaction by:
> G(a)= H(a) - TS
> G(b)= H(b) - TS
> G(c)= H(c) - TS
>
> What is the correct way to calculate G (reaction)?
> G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated jobs
> or
> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job and
> separated from each other by 50A
>
> These two methods are different and giving different results at the same level
> of calculation. Counting TS twice in the first equation may be a reason, but in
> the second equation accounting rotation and transition degrees is also a
> problem.
> Is there another equation you use?
> Any kind of help would be appreciated
> Thanks in advance
> Flak
>
>
>
From owner-chemistry@ccl.net Fri Aug 6 14:54:01 2010
From: "Jamin Krinsky jamink(-)berkeley.edu" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42466-100806133422-2533-eqbexNY9/giggKLUfHlBDg^^^server.ccl.net>
X-Original-From: Jamin Krinsky <jamink ~~ berkeley.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 6 Aug 2010 10:34:14 -0700
MIME-Version: 1.0
Sent to CCL by: Jamin Krinsky [jamink^berkeley.edu]
Just adding up the free energies like that gives incorrect entropies,
as the entropy difference associated with the change in molecularity
is not accounted for. There has been some talk in the literature about
correction factors for this, but I can't seem to remember any
references. It is partially because of this that you don't see many
papers using free energies in studying reaction pathways...
Jamin
On Fri, Aug 6, 2010 at 8:38 AM, Charles Johnson cjohns98^-^slu.edu
<owner-chemistry-x-ccl.net> wrote:
> I would first calculate G for each, A, B and C individually.� Then use the
> equation G(rxn)=G(c)-(G(a)+G(b)).
>
> hope that helps
>
> On Fri, Aug 6, 2010 at 9:37 AM, William Flak williamflak++yahoo.com
> <owner-chemistry a ccl.net> wrote:
>>
>> Sent to CCL by: "William �Flak" [williamflak^^yahoo.com]
>> Dear CCL users
>> This may be a trivial question, I am not a student but I got confused and
>> my
>> colleagues here say different answers.
>> For A + B ---> C, comparing the Gibbs free energy for this reaction by:
>> G(a)= H(a) - TS
>> G(b)= H(b) - TS
>> G(c)= H(c) - TS
>>
>> What is the correct way to calculate G (reaction)?
>> �G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated
>> jobs
>> or
>> �G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job
>> and
>> separated from each other by 50A
>>
>> These two methods are different and giving different results at the same
>> level
>> of calculation. Counting TS twice in the first equation may be a reason,
>> but in
>> the second equation accounting rotation and transition degrees is also a
>> problem.
>> Is there another equation you use?
>> Any kind of help would be appreciated
>> Thanks in advance
>> Flak>> E-mail to subscribers: CHEMISTRY a ccl.net or use:
>> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>>
>> E-mail to administrators: CHEMISTRY-REQUEST a ccl.net or use
>> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> � � �http://www.ccl.net/chemistry/sub_unsub.shtml>> � � �http://www.ccl.net/spammers.txt>>
>>
>
>
>
> --
> Charles A. Johnson
> Graduate Student
> Department of Chemistry
>
>
>
--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink-x-berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu
From owner-chemistry@ccl.net Fri Aug 6 16:07:00 2010
From: "Christopher Cramer cramer*o*umn.edu" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42467-100806160537-29384-jQoQ5iNvTNKERCWBkJ5xYw]=[server.ccl.net>
X-Original-From: Christopher Cramer <cramer/a\umn.edu>
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Date: Fri, 6 Aug 2010 22:05:20 +0200
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Sent to CCL by: Christopher Cramer [cramer[A]umn.edu]
I confess to being somewhat puzzled by some of the responses to the
original question.
Within the ideal-gas, rigid-rotator, harmonic-oscillator
approximation, the free energy of a molecule "A" is fairly well
defined once one has accomplished a computation of vibrational
frequencies for an optimized geometry (I say fairly only because A may
have multiple conformers, and in practice researchers often use only
one). Thus, the partition functions for the (i) electronic, (ii)
translational, (iii) rotational, and (iv) vibrational contributions to
the energy are taken as (i) the electronic state degeneracy (assuming
that, at relevant temperatures, excited states are not populated),
(ii) dependent only on the molecular weight (particle in a box
translation, with volume of the box defining the standard state),
(iii) dependent only on the principal moments of inertia (rigid
rotator approximation), and (iv) dependent only on the vibrational
frequencies (QM harmonic oscillator approximation), respectively.
There is no ambiguity associated with molecularity. This is textbook
undergraduate thermodynamics for an ideal gas. Textbooks also show
that these approximations work quite well for most simple gases at low
pressures (where reasonable "ideality" is observed). It is not "double-
counting" T-deltaS to have it for both A and B in a reaction where A +
B --> C, rather it is accurate. You will "lose" considerable entropy
in the bimolecular association. Of course, it is important to remember
that the computed value is a standard-state value. That is, it is the
free energy change for all species at the same standard-state
concentration (which, for a gas, is often expressed as a pressure). In
a "real" reaction, the pressure (if gaseous) might well change, and
one would need to account for this in computing the degree to which
the reaction proceeds given a particular set of starting partial
pressures and/or ending pressure.
As for constraining the A and B molecules to be 50 ang apart, that is
equivalent to assigning the "reactant" to be an ideal gas that is
indeed a species A - - - - B that is, hmm, shall we call it,
bifragmental? Beyond the rather bizarre idea of this as the elementary
constituent of the gas, there would also be the practical issue that
many of the vibrations computed for this species would be essentially
zero (because they refer to translations and rotations of each
fragment within the "complex"), and the use of the harmonic oscillator
approximation would be disastrous in such a case.
All of the above being said, certainly one can improve on the "usual"
approximations, e.g., by replacing the harmonic oscillator partition
function with free or hindered rotor partition functions where
appropriate, or by considering anharmonic corrections, or by including
centrifugal distortion in the rotational partition function, or by
including low-energy spin-orbit states. Many possibilities. And, there
certainly ARE some ambiguities introduced if we consider attempting to
include solvation effects by, say, a continuum model (how do the
"rotations" of a solute in a continuum solvent correspond to actual
"librations" in a supermolecular system?). But, those are subjects for
an alternative discussion.
Best regards,
Chris
On Aug 6, 2010, at 7:34 PM, Jamin Krinsky jamink(-)berkeley.edu wrote:
>
> Sent to CCL by: Jamin Krinsky [jamink^berkeley.edu]
> Just adding up the free energies like that gives incorrect entropies,
> as the entropy difference associated with the change in molecularity
> is not accounted for. There has been some talk in the literature about
> correction factors for this, but I can't seem to remember any
> references. It is partially because of this that you don't see many
> papers using free energies in studying reaction pathways...
>
> Jamin
>
>
> On Fri, Aug 6, 2010 at 8:38 AM, Charles Johnson cjohns98^-^slu.edu
> <owner-chemistry!=!ccl.net> wrote:
>> I would first calculate G for each, A, B and C individually. Then
>> use the
>> equation G(rxn)=G(c)-(G(a)+G(b)).
>>
>> hope that helps
>>
>> On Fri, Aug 6, 2010 at 9:37 AM, William Flak williamflak++yahoo.com
>> <owner-chemistry a ccl.net> wrote:
>>>
>>> Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
>>> Dear CCL users
>>> This may be a trivial question, I am not a student but I got
>>> confused and
>>> my
>>> colleagues here say different answers.
>>> For A + B ---> C, comparing the Gibbs free energy for this
>>> reaction by:
>>> G(a)= H(a) - TS
>>> G(b)= H(b) - TS
>>> G(c)= H(c) - TS
>>>
>>> What is the correct way to calculate G (reaction)?
>>> G(reaction) = G(c) - G(a) - G(b) here A and B calculated in
>>> separated
>>> jobs
>>> or
>>> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one
>>> single job
>>> and
>>> separated from each other by 50A
>>>
>>> These two methods are different and giving different results at
>>> the same
>>> level
>>> of calculation. Counting TS twice in the first equation may be a
>>> reason,
>>> but in
>>> the second equation accounting rotation and transition degrees is
>>> also a
>>> problem.
>>> Is there another equation you use?
>>> Any kind of help would be appreciated
>>> Thanks in advance
>>> Flak>> E-mail to subscribers: CHEMISTRY a ccl.net or use:>>>
>>> E-mail to administrators: CHEMISTRY-REQUEST a ccl.net or use>>
>>>
>>
>>
>>
>> --
>> Charles A. Johnson
>> Graduate Student
>> Department of Chemistry
>>
>>
>>
>
>
>
> --
> Jamin L Krinsky, Ph.D.
> Molecular Graphics and Computation Facility
> 175 Tan Hall, University of California, Berkeley, CA 94720
> jamink!=!berkeley.edu, 510-643-0616
> http://glab.cchem.berkeley.edu
>
>
>
> -= This is automatically added to each message by the mailing script
> =-
> To recover the email address of the author of the message, please
> change> Conferences: http://server.ccl.net/chemistry/announcements/
> conferences/>
>
--
Christopher J. Cramer
Elmore H. Northey Professor
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone: (612) 624-0859 || FAX: (612) 626-7541
Mobile: (952) 297-2575
email: cramer..umn.edu
jabber: cramer..jabber.umn.edu
http://pollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
of Computational Chemistry: Theories and Models, 2nd Edition")
From owner-chemistry@ccl.net Fri Aug 6 16:42:01 2010
From: "Jim Kress ccl_nospam*kressworks.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42468-100806163549-2667-j4/kCW3ZZPy7I9aAJqu87w[a]server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam%a%kressworks.com>
Content-Language: en-us
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charset="windows-1251"
Date: Fri, 6 Aug 2010 16:35:35 -0400
MIME-Version: 1.0
Sent to CCL by: "Jim Kress" [ccl_nospam*o*kressworks.com]
Does this help?
Free Energy Barrier for Molecular Motions in
Bistable [2]Rotaxane Molecular Electronic Devices�
Hyungjun Kim, William A. Goddard III, Seung Soon Jang,
William R. Dichtel, James R. Heath, and J. Fraser Stoddart
J. Phys. Chem. A, 2009, 113 (10), 2136-2143� DOI: 10.1021/jp809213m �
Publication Date (Web): 18 February 2009
It does provide a methodology for calculating delta G, which is what you
really need.
Jim
-----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com!A!ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com!A!ccl.net] On Behalf Of
William Flak williamflak++yahoo.com
Sent: Friday, August 06, 2010 10:37 AM
To: Kress, Jim
Subject: CCL: Gibbs free energy
Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
Dear CCL users
This may be a trivial question, I am not a student but I got confused and my
colleagues here say different answers.
For A + B ---> C, comparing the Gibbs free energy for this reaction by:
G(a)= H(a) - TS
G(b)= H(b) - TS
G(c)= H(c) - TS
What is the correct way to calculate G (reaction)?
G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated jobs
or
G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job
and
separated from each other by 50A
These two methods are different and giving different results at the same
level
of calculation. Counting TS twice in the first equation may be a reason, but
in
the second equation accounting rotation and transition degrees is also a
problem.
Is there another equation you use?
Any kind of help would be appreciated
Thanks in advance
Flakhttp://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 Fri Aug 6 18:09:01 2010
From: "William Flak williamflak===yahoo.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42469-100806153932-10926-uUtQ0sDhHdMOb7NI6DtZKA\a/server.ccl.net>
X-Original-From: William Flak <williamflak^^yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 6 Aug 2010 12:39:24 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: William Flak [williamflak(-)yahoo.com]
Dear Charles, Ibrahim , Richard, and Ga
Thank you for replying.
Great!!! Let's say the calculation was done using Size-consistent method, so:
Case I:
A + B ---> C
G(reaction) = G(c) - G(a) - G(b)
G = H -TS, so
G(reaction) = H(c) - H(a) - H(b) - T [S(c) - S(a) - S(b)]
H = E + RT, so
G(reaction) = E(c) - E(a) - E(b) + RT - T [S(c) - S(a) - S(b)]
Case II:
A + B ---> C
G(reaction) = G(c) - G(a) - G(b)
G = H -TS, so
G(reaction) = H(c) - H(ab) - T [S(c) - S(ab)]
H = E + RT, so
G(reaction) = E(c) - E(ab) - T [S(c) - S(ab)]
Ga mentioned that the two ways are possible if the method is size consistent,
ie, if E(a) + E(b) = E(ab)
so,
E(c) - E(a) - E(b) + RT - T [S(c) - S(a) - S(b)] = E(c) - E(ab) - T [S(c) - S(ab)]
So
RT - T [S(a) - S(b)] = - T S(ab)
is that right?
Ibrahim mentioned, rotation and transition degrees will be different in both cases, and should be counted, how?
Any explanation would be appreciated.
Thanks in advance
Flak
--- On Fri, 8/6/10, Ol Ga eurisco1!=!pochta.ru <owner-chemistry!A!ccl.net> wrote:
> From: Ol Ga eurisco1!=!pochta.ru <owner-chemistry!A!ccl.net>
> Subject: CCL: Gibbs free energy
> To: "Flak, William " <williamflak!A!yahoo.com>
> Date: Friday, August 6, 2010, 3:47 PM
>
> Sent to CCL by: "Ol� Ga" [eurisco1 .. pochta.ru]
> Dear William Flak,
>
> First of all we should answer how to calculate energy of
> this reaction. If the QC method is not size-consistent
> (e.g., available DFT functionals), the second strategy
> defined by your words
> > G(reaction) = G(c) - G((a)&(b)) here A and B
> calculated in one single job and� > separated from
> each other by 50A
>
> is completely wrong. In this case it is necessary to make 3
> separate calculations.
>
> If the QC method is size-consistent, in principle it is
> possible to apply both strategies. I would note that 50 A is
> too crude, maybe 7-10 A is more convenient.
>
> About entropy of the reaction: really it is difficult to
> calculate with high precision.
>
> Sincerely,
> Ol Ga
>
> --------------------------------------------------
> > From: "William Flak williamflak++yahoo.com"
> <owner-chemistry[A]ccl.net>
> Sent: Friday, August 06, 2010 6:37 PM
> To: "Ga, Ol " <eurisco1[A]pochta.ru>
> Subject: CCL: Gibbs free energy
>
> >
> >
> > Sent to CCL by: "William� Flak"
> [williamflak^^yahoo.com]
> > Dear CCL users
> > This may be a trivial question, I am not a student but
> I got confused and my
> > colleagues here say different answers.
> > For A + B ---> C, comparing the Gibbs free energy
> for this reaction by:
> > G(a)= H(a) - TS
> > G(b)= H(b) - TS
> > G(c)= H(c) - TS
> >
> > What is the correct way to calculate G (reaction)?
> > G(reaction) = G(c) - G(a) - G(b) here A and B
> calculated in separated jobs
> > or
> > G(reaction) = G(c) - G((a)&(b)) here A and B
> calculated in one single job and
> > separated from each other by 50A
> >
> > These two methods are different and giving different
> results at the same level
> > of calculation. Counting TS twice in the first
> equation may be a reason, but in
> > the second equation accounting rotation and transition
> degrees is also a
> > problem.
> > Is there another equation you use?
> > Any kind of help would be appreciated
> > Thanks in advance
> > Flak
> >
> >
> >
>
>
>
> -= This is automatically added to each message by the
> mailing script =-
> To recover the email address of the author of the message,
> please change
> the strange characters on the top line to the !A! sign. You
> can also>
> E-mail to subscribers: CHEMISTRY!A!ccl.net
> or use:
> � � �>
> E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net
> or use
> � � �> � � �> � � �>
>
>
From owner-chemistry@ccl.net Fri Aug 6 18:44:00 2010
From: "Michael Gilson mgilson++ucsd.edu" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42470-100806154327-14382-Jw17QOU1RiSfNmdS5aG23w(!)server.ccl.net>
X-Original-From: Michael Gilson <mgilson%x%ucsd.edu>
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Date: Fri, 06 Aug 2010 12:44:44 -0700
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Sent to CCL by: Michael Gilson [mgilson..ucsd.edu]
I suspect that if you just separate the two species, the standard state
will become problematic. DG should be appropriate to 1 atm of each
species, and making the dimer (though separated) into a species at 1 atm
-- my guess as to the outcome -- will not be right.
Regards,
Mike
On 8/6/10 8:47 AM, Ol Ga eurisco1!=!pochta.ru wrote:
> Sent to CCL by: "Ol Ga" [eurisco1 .. pochta.ru]
> Dear William Flak,
>
> First of all we should answer how to calculate energy of this reaction. If the QC method is not size-consistent (e.g., available DFT functionals), the second strategy defined by your words
>
>> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job and> separated from each other by 50A
>>
> is completely wrong. In this case it is necessary to make 3 separate calculations.
>
> If the QC method is size-consistent, in principle it is possible to apply both strategies. I would note that 50 A is too crude, maybe 7-10 A is more convenient.
>
> About entropy of the reaction: really it is difficult to calculate with high precision.
>
> Sincerely,
> Ol Ga
>
> --------------------------------------------------
>
>> From: "William Flak williamflak++yahoo.com"<owner-chemistry[A]ccl.net>
>>
> Sent: Friday, August 06, 2010 6:37 PM
> To: "Ga, Ol "<eurisco1[A]pochta.ru>
> Subject: CCL: Gibbs free energy
>
>
>>
>> Sent to CCL by: "William Flak" [williamflak^^yahoo.com]
>> Dear CCL users
>> This may be a trivial question, I am not a student but I got confused and my
>> colleagues here say different answers.
>> For A + B ---> C, comparing the Gibbs free energy for this reaction by:
>> G(a)= H(a) - TS
>> G(b)= H(b) - TS
>> G(c)= H(c) - TS
>>
>> What is the correct way to calculate G (reaction)?
>> G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated jobs
>> or
>> G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single job and
>> separated from each other by 50A
>>
>> These two methods are different and giving different results at the same level
>> of calculation. Counting TS twice in the first equation may be a reason, but in
>> the second equation accounting rotation and transition degrees is also a
>> problem.
>> Is there another equation you use?
>> Any kind of help would be appreciated
>> Thanks in advance
>> Flak>
>
>
--
Michael K. Gilson, M.D., Ph.D.
Professor
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California San Diego
9500 Gilman Drive, MC 0736
La Jolla, CA 92093-0736
voice: 858-822-0622
From owner-chemistry@ccl.net Fri Aug 6 19:19:01 2010
From: "William Flak williamflak[-]yahoo.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42471-100806154032-11792-rlFVhj5HFNWX/QapXKUYuA]![server.ccl.net>
X-Original-From: William Flak <williamflak a yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 6 Aug 2010 12:39:46 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: William Flak [williamflak()yahoo.com]
Dear Charles, Ibrahim , Richard, and Ga
Thank you for replying.
Great!!! Let's say the calculation was done using Size-consistent method, so:
Case I:
A + B ---> C
G(reaction) = G(c) - G(a) - G(b)
G = H -TS, so
G(reaction) = H(c) - H(a) - H(b) - T [S(c) - S(a) - S(b)]
H = E + RT, so
G(reaction) = E(c) - E(a) - E(b) + RT - T [S(c) - S(a) - S(b)]
Case II:
A + B ---> C
G(reaction) = G(c) - G(a) - G(b)
G = H -TS, so
G(reaction) = H(c) - H(ab) - T [S(c) - S(ab)]
H = E + RT, so
G(reaction) = E(c) - E(ab) - T [S(c) - S(ab)]
Ga mentioned that the two ways are possible if the method is size consistent,
ie, if E(a) + E(b) = E(ab)
so,
E(c) - E(a) - E(b) + RT - T [S(c) - S(a) - S(b)] = E(c) - E(ab) - T [S(c) - S(ab)]
So
RT - T [S(a) - S(b)] = - T S(ab)
is that right?
Ibrahim mentioned, rotation and transition degrees will be different in both cases, and should be counted, how?
Any explanation would be appreciated.
Thanks in advance
Flak
--- On Fri, 8/6/10, Ol Ga eurisco1!=!pochta.ru <owner-chemistry _ ccl.net> wrote:
> From: Ol Ga eurisco1!=!pochta.ru <owner-chemistry _ ccl.net>
> Subject: CCL: Gibbs free energy
> To: "Flak, William " <williamflak _ yahoo.com>
> Date: Friday, August 6, 2010, 3:47 PM
>
> Sent to CCL by: "Ol� Ga" [eurisco1 .. pochta.ru]
> Dear William Flak,
>
> First of all we should answer how to calculate energy of
> this reaction. If the QC method is not size-consistent
> (e.g., available DFT functionals), the second strategy
> defined by your words
> > G(reaction) = G(c) - G((a)&(b)) here A and B
> calculated in one single job and� > separated from
> each other by 50A
>
> is completely wrong. In this case it is necessary to make 3
> separate calculations.
>
> If the QC method is size-consistent, in principle it is
> possible to apply both strategies. I would note that 50 A is
> too crude, maybe 7-10 A is more convenient.
>
> About entropy of the reaction: really it is difficult to
> calculate with high precision.
>
> Sincerely,
> Ol Ga
>
> --------------------------------------------------
> > From: "William Flak williamflak++yahoo.com"
> <owner-chemistry[A]ccl.net>
> Sent: Friday, August 06, 2010 6:37 PM
> To: "Ga, Ol " <eurisco1[A]pochta.ru>
> Subject: CCL: Gibbs free energy
>
> >
> >
> > Sent to CCL by: "William� Flak"
> [williamflak^^yahoo.com]
> > Dear CCL users
> > This may be a trivial question, I am not a student but
> I got confused and my
> > colleagues here say different answers.
> > For A + B ---> C, comparing the Gibbs free energy
> for this reaction by:
> > G(a)= H(a) - TS
> > G(b)= H(b) - TS
> > G(c)= H(c) - TS
> >
> > What is the correct way to calculate G (reaction)?
> > G(reaction) = G(c) - G(a) - G(b) here A and B
> calculated in separated jobs
> > or
> > G(reaction) = G(c) - G((a)&(b)) here A and B
> calculated in one single job and
> > separated from each other by 50A
> >
> > These two methods are different and giving different
> results at the same level
> > of calculation. Counting TS twice in the first
> equation may be a reason, but in
> > the second equation accounting rotation and transition
> degrees is also a
> > problem.
> > Is there another equation you use?
> > Any kind of help would be appreciated
> > Thanks in advance
> > Flak
> >
> >
> >
>
>
>
> -= This is automatically added to each message by the
> mailing script =-
> 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:
> � � �>
> E-mail to administrators: CHEMISTRY-REQUEST _ ccl.net
> or use
> � � �> � � �> � � �>
>
>
From owner-chemistry@ccl.net Fri Aug 6 19:53:01 2010
From: "Kalju Kahn kalju(a)chem.ucsb.edu" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL:G: Reaction Rate as a function of Pressure
Message-Id: <-42472-100806180542-17526-4GL2XjaGBWuL3N92sQYL4g-.-server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju{=}chem.ucsb.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Fri, 6 Aug 2010 15:05:27 -0700
MIME-Version: 1.0
Sent to CCL by: "Kalju Kahn" [kalju|,|chem.ucsb.edu]
Thomas,
I think there is a simpler way than resorting to RRKM for what you are
trying to do (at least for the equilibrium constant, and reactions in
solution). The short answer is that you need to look at activation and
reaction volumes for the pressure dependence. Read on for a long answer
:)
> This is where I have a problem. The frequency outcome as a function of
> temperature is fine and I have no problems with it, but the pressure
> outcome is really puzzling. My results seem to indicate that all the
> thermodynamic quantities that I calculate have almost negligible
> dependence on pressure (especially the frequencies that remain unchanged
> for the same temperature). I am interested in temperature ranges of the
> order 300K-800K and pressures from 1bar to 3000bars.
The pressure outcome is easy to understand: Gaussian calculates entropic
and thermal correction to free energy assuming an ideal gas. In this
case, rotational and vibrational contributions are pressure-independent
(you can Google Books "Kahn Plaxco Recognition Receptors in Biosensors",
pg 31); only translational entropy has some pressure-dependence. This may
not be appropriate model for you: gas at 300K and 3000 bars is far from
ideal.
On the other hand, it may be just good enough. Vibrational frequencies
(these depend on the curvature of molecular PES) even in the real gas are
not very pressure-dependent, the may change a few cm-1 or so if you go
> from 1 bar to 3000 bars using inert gas for pressure. This will not
change your equilibrium significantly. Rotational contributions to
entropy depend on the shape of the molecule, and the structure of small
molecules (e.g. your tert-butoxy radical) is not going to be
pressure-dependent. So your error comes mainly by approximating
translational entropy of a real gas with the ideal gas formula.
As far as the pressure dependence of equilibrium goes, have you evaluated
the change in the volume when going from reactants and products? There is
a basic thermodynamic relationship that says: d(ln K)/dP = -deltaV/RT.
This actually falls out from from the dependence of free energy on
pressure, but hides some of the complications discussed above.
By the way, a similar relationship can be postulated for rates:
d(ln k)/dP = -(V_ts-V_react)/RT. The difference in the volumes of the
transition state and the reactant is what matters here. However, in the
gas phase the rate increase with pressure arises mainly from collisional
energy transfer; this is where RRKM comes in. Only at the high-pressure
limit is the activation volume relevant. Thus, if you need to model the
rate of unimolecular gas-phase decomposition over a broad pressure range
you need to use RRKM.
> I can imagine that the solvent will be heavily affected by the pressure,
> but I was expecting to see some effect (a bit smaller but still
> measurable) in the gas as well.
I do not share this opinion. The pressure effect on rates in solutions is
typically small because the collisional energy transfer efficiency is
near-maximal already at normal pressures. So, here the activation volume
plays a larger role, but you need to worry also about things like change
in solution viscosity and dielectric constant with pressure.
The pressure effect on chemical equilibrium is not large either.
Nevertheless, there are some interesting examples of pressure induced
shifts of equilibrium: many proteins unfold at very high pressures in
water because unfolded state is more compact in water (isn't this
surprising). As you probably guessed from the protein example,
calculation of reaction volumes can be tricky because you need to properly
describe solvation of your reactant and the two products. Do do this
properly, one could perform NPT free energy perturbation (called FEP, and
I am talking about force fields, not QM here) of the reactant to products
and measure the change in the volume of the simulation box.
The proper calculation of activation volume via NPT simulations is
trickier. The lifetime of TS is so short that the solvent molecules may
or may not reorganize themselves around the TS. If they do not, you can
argue that thee is no effect at all because the volume of the solution des
not change during the reaction. If water molecules can translate during
the TS formation, the solution expands, and there is a pressure effect.
You do not need NPT simulation for that; assumption that the change in the
solution volume is equal to the change in the V(TS) - V(reactant) seems
reasonable. If water molecules can reorient and solvate the TS
differently than the reactant, then you need an NPT simulation to capture
this effect. But because TS can't be described well by force fields, you
need a QM/MM FEP. Not impossible, but far from trivial.
In summary:
* gas phase equilibrium: calculate molecular volumes with a QM code such
as Gaussian
* gas phase rate: RRKM
* solution phase equilibrium: calculate molecular volumes of implicitly
solvated molecules with a QM code such as Gaussian after optimizing
molecules with a dielectric constant appropriate for a given pressure. If
this does not yield desired result perform NPT FEP simulations at
different pressures to describe changes due to solvent structure around
solutes.
* solution phase rate: calculate volumes of TS and the reactant with a QM
code such as Gaussian after optimizing structures with an appropriate
pressure-dependent dielectric. Correct for viscosity dependence (maybe
not important for unimolecular irreversible process) based on exp data; if
this does not yield desired results make it a Ph.D. project for a
talented student.
Hope this helps,
Kalju
> Thanks a lot for all the answers guys. They're most appreciated. I will
> look for the relevant software you recommended and I will also check the
> literature on the subject again to see what I can dig up.
>
> Alain the calculations that I have done so far are in the gas phase, and I
> am doing them in a solvent as we speak. I can imagine that the solvent
> will be heavily affected by the pressure, but I was expecting to see some
> effect (a bit smaller but still measurable) in the gas as well.
>
> Again thanks a lot
>
> Thomas
>
>
> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com(-)ccl.net
> [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com(-)ccl.net] On
> Behalf Of ABHISHEK SHAHI shahi.abhishek1984[A]gmail.com
> Sent: Friday, August 06, 2010 12:08 PM
> To: Gkourmpis, Thomas
> Subject: CCL:G: Reaction Rate as a function of Pressure
>
> Hi Thomas
> Fortran codes are available for temperature dependence rate constant
> (TST theory) and energy dependence rate constant (RRKM theory).But I
> don't know any pressure dependence program for rate constant
> calculation.let me know if you get something. For RRKM calculation,
> follow the following LINK. And if its not helpfull to you then write to
> auther for Program(free)
>
> ONLINE RRKM CALCULATOR<http://phd.marginean.net/rrkm.html>.
>
>
> With regards;
> ABHISHEK SHAHI [http://e/softbank_ne_jp.7D9]
> Ph. D. student
> Department of Inorganic and Physical Chemistry
> IISc bangalore-12
> [http://e/ezweb_ne_jp.523] : 080-2293-2384(lab)
> Official E-mail: shahi()
> ipc.iisc.ernet.in<mailto:shahi()%20ipc.iisc.ernet.in>
> CC: shahi.abhishek1984()
> gmail.com<mailto:shahi.abhishek1984()%20gmail.com>
>
> On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpis, Thomas
> Thomas.Gkourmpis-,-borealisgroup.com<http://borealisgroup.com>
> <owner-chemistry() ccl.net<mailto:owner-chemistry()%20ccl.net>> wrote:
>
> Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis .
> borealisgroup.com<http://borealisgroup.com>]
> Thanks for the answer. I was actually afraid that Gaussian will not be up
> to the job to get these types of correlations. Are you aware of a software
> that can perform the RRKM/master equation analysis?
>
> Thanks again
>
> Thomas
>
> -----Original Message-----
>> From:
>> owner-chemistry+thomas.gkourmpis==borealisgroup.com_._ccl.net<http://ccl.net>
>> [mailto:owner-chemistry+thomas.gkourmpis<mailto:owner-chemistry%2Bthomas.gkourmpis>==borealisgroup.com_._ccl.net<http://ccl.net>]
>> On Behalf Of Simmie, John
>> john.simmie[#]nuigalway.ie<http://nuigalway.ie>
> Sent: Friday, August 06, 2010 5:26 AM
> To: Gkourmpis, Thomas
> Subject: CCL:G: Reaction Rate as a function of Pressure
>
> Thomas
> You are already calculating the reaction rate at the high-pressure limit
> to get the pressue dependent rate constants you need to employ
> RRKM/master
> equation theory ... which lies outside the province of Gaussian, Molpro,
> etc
>
> J Simmie::Combustion Chemistry Centre::NUI Galway Ireland
>
>
> -----Original Message-----
>> From:
>> owner-chemistry+john.simmie==nuigalway.ie-.-ccl.net<http://ccl.net> on
>> behalf of Thomas Gkourmpis
>> thomas.gkourmpis(~)borealisgroup.com<http://borealisgroup.com>
> Sent: Thu 05/08/2010 14:37
> To: Simmie, John
> Subject: CCL:G: Reaction Rate as a function of Pressure
>
>
> Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis *
> borealisgroup.com<http://borealisgroup.com>]
> Hello everyone
> I have a question to ask regarding the pressure and temperature dependence
> on the reaction rate. I am trying to calculate the rate constant of a beta
> scission in a radical (tertbutoxy radical) obtained by the decomposition
> of a peroxide. I am using Gaussian for this job and I have no problem in
> locating the minimum energy configurations for products, reactant(s) and
> transition states. After the final structures have been obtained I am
> running a frequency calculation as a function of pressure and temperature
> to obtain the relevant frequencies, Gibbs Free Energies and partition
> functions I need for the Arrhenius equation.
>
> This is where I have a problem. The frequency outcome as a function of
> temperature is fine and I have no problems with it, but the pressure
> outcome is really puzzling. My results seem to indicate that all the
> thermodynamic quantities that I calculate have almost negligible
> dependence on pressure (especially the frequencies that remain unchanged
> for the same temperature). I am interested in temperature ranges of the
> order 300K-800K and pressures from 1bar to 3000bars. I know from
> experimental data that the reaction constant does change as a function of
> pressure (it gets shifted towards the right as pressure increases), but my
> calculations does not seem to be able to reproduce this phenomenon.
> One of the reasons I can think about this is the fact that all the
> thermochemical calculations in Gaussian are done under the
> Born-Oppenheimer approximation, but I am not sure if this is the only
> reason (I might be missing something else).
>
> Therefore the favour I want to ask is this: Can anyone tell me if this is
> an effect due only to the approximation I am using? Furthermore if this is
> the case can anybody please suggest any possible ways to apply corrections
> to this approximation for high pressures?
>
> Thanks a lot in advance
> Thomashttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D--<http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp:/www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D-->
>
>
>
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> -= This is automatically added to each message by the mailing script
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>
> E-mail to subscribers: CHEMISTRY() ccl.net<mailto:CHEMISTRY()%20ccl.net>
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> ccl.net<mailto:CHEMISTRY-REQUEST()%20ccl.net> or use> <br>
>
>
>
>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106
From owner-chemistry@ccl.net Fri Aug 6 20:29:01 2010
From: "Jamin Krinsky jamink ~~ berkeley.edu" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Gibbs free energy
Message-Id: <-42473-100806181506-30824-NMxiVRLpZY/HlHUeri0fdw+*+server.ccl.net>
X-Original-From: Jamin Krinsky <jamink:-:berkeley.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 6 Aug 2010 15:14:59 -0700
MIME-Version: 1.0
Sent to CCL by: Jamin Krinsky [jamink a berkeley.edu]
I apologize for the vague post concerning molecularity in this case,
it is irresponsible to post here without first thinking about it. What
I was referring to is that it is common to try to model pathways that
are actually operative in the condensed phase using a gas-phase (or
implicit solvent) model, and while this can often give enthalpies
reasonably in agreement with experimental (solution) data, the
entropies will not correspond with the experimental values. I'm badly
paraphrasing Tom Ziegler (Inorg. Chem. 2002, 41, 6614-6622) here.
Sorry if I am still being too vague, and Dr. Cramer obviously knows
much more about this than I do ("Essentials of Computational
Chemistry" is on my bookshelf, maybe it's time to give it another
look).
Jamin
On Fri, Aug 6, 2010 at 1:05 PM, Christopher Cramer cramer*o*umn.edu
<owner-chemistry~!~ccl.net> wrote:
>
> Sent to CCL by: Christopher Cramer [cramer[A]umn.edu]
> I confess to being somewhat puzzled by some of the responses to the original
> question.
>
> Within the ideal-gas, rigid-rotator, harmonic-oscillator approximation, the
> free energy of a molecule "A" is fairly well defined once one has
> accomplished a computation of vibrational frequencies for an optimized
> geometry (I say fairly only because A may have multiple conformers, and in
> practice researchers often use only one). Thus, the partition functions for
> the (i) electronic, (ii) translational, (iii) rotational, and (iv)
> vibrational contributions to the energy are taken as (i) the electronic
> state degeneracy (assuming that, at relevant temperatures, excited states
> are not populated), (ii) dependent only on the molecular weight (particle in
> a box translation, with volume of the box defining the standard state),
> (iii) dependent only on the principal moments of inertia (rigid rotator
> approximation), and (iv) dependent only on the vibrational frequencies (QM
> harmonic oscillator approximation), respectively.
>
> There is no ambiguity associated with molecularity. This is textbook
> undergraduate thermodynamics for an ideal gas. Textbooks also show that
> these approximations work quite well for most simple gases at low pressures
> (where reasonable "ideality" is observed). It is not "double-counting"
> T-deltaS to have it for both A and B in a reaction where A + B --> C, rather
> it is accurate. You will "lose" considerable entropy in the bimolecular
> association. Of course, it is important to remember that the computed value
> is a standard-state value. That is, it is the free energy change for all
> species at the same standard-state concentration (which, for a gas, is often
> expressed as a pressure). In a "real" reaction, the pressure (if gaseous)
> might well change, and one would need to account for this in computing the
> degree to which the reaction proceeds given a particular set of starting
> partial pressures and/or ending pressure.
>
> As for constraining the A and B molecules to be 50 ang apart, that is
> equivalent to assigning the "reactant" to be an ideal gas that is indeed a
> species A - - - - B that is, hmm, shall we call it, bifragmental? Beyond the
> rather bizarre idea of this as the elementary constituent of the gas, there
> would also be the practical issue that many of the vibrations computed for
> this species would be essentially zero (because they refer to translations
> and rotations of each fragment within the "complex"), and the use of the
> harmonic oscillator approximation would be disastrous in such a case.
>
> All of the above being said, certainly one can improve on the "usual"
> approximations, e.g., by replacing the harmonic oscillator partition
> function with free or hindered rotor partition functions where appropriate,
> or by considering anharmonic corrections, or by including centrifugal
> distortion in the rotational partition function, or by including low-energy
> spin-orbit states. Many possibilities. And, there certainly ARE some
> ambiguities introduced if we consider attempting to include solvation
> effects by, say, a continuum model (how do the "rotations" of a solute in a
> continuum solvent correspond to actual "librations" in a supermolecular
> system?). But, those are subjects for an alternative discussion.
>
> Best regards,
>
> Chris
>
> On Aug 6, 2010, at 7:34 PM, Jamin Krinsky jamink(-)berkeley.edu wrote:
>
>>
>> Sent to CCL by: Jamin Krinsky [jamink^berkeley.edu]
>> Just adding up the free energies like that gives incorrect entropies,
>> as the entropy difference associated with the change in molecularity
>> is not accounted for. There has been some talk in the literature about
>> correction factors for this, but I can't seem to remember any
>> references. It is partially because of this that you don't see many
>> papers using free energies in studying reaction pathways...
>>
>> Jamin
>>
>>
>> On Fri, Aug 6, 2010 at 8:38 AM, Charles Johnson cjohns98^-^slu.edu
>> <owner-chemistry!=!ccl.net> wrote:
>>>
>>> I would first calculate G for each, A, B and C individually. �Then use
>>> the
>>> equation G(rxn)=G(c)-(G(a)+G(b)).
>>>
>>> hope that helps
>>>
>>> On Fri, Aug 6, 2010 at 9:37 AM, William Flak williamflak++yahoo.com
>>> <owner-chemistry a ccl.net> wrote:
>>>>
>>>> Sent to CCL by: "William �Flak" [williamflak^^yahoo.com]
>>>> Dear CCL users
>>>> This may be a trivial question, I am not a student but I got confused
>>>> and
>>>> my
>>>> colleagues here say different answers.
>>>> For A + B ---> C, comparing the Gibbs free energy for this reaction by:
>>>> G(a)= H(a) - TS
>>>> G(b)= H(b) - TS
>>>> G(c)= H(c) - TS
>>>>
>>>> What is the correct way to calculate G (reaction)?
>>>> �G(reaction) = G(c) - G(a) - G(b) here A and B calculated in separated
>>>> jobs
>>>> or
>>>> �G(reaction) = G(c) - G((a)&(b)) here A and B calculated in one single
>>>> job
>>>> and
>>>> separated from each other by 50A
>>>>
>>>> These two methods are different and giving different results at the same
>>>> level
>>>> of calculation. Counting TS twice in the first equation may be a reason,
>>>> but in
>>>> the second equation accounting rotation and transition degrees is also a
>>>> problem.
>>>> Is there another equation you use?
>>>> Any kind of help would be appreciated
>>>> Thanks in advance
>>>> Flak>> E-mail to subscribers: CHEMISTRY a ccl.net or use:>>>
>>>> E-mail to administrators: CHEMISTRY-REQUEST a ccl.net or use>>
>>>>
>>>
>>>
>>>
>>> --
>>> Charles A. Johnson
>>> Graduate Student
>>> Department of Chemistry
>>>
>>>
>>>
>>
>>
>>
>> --
>> Jamin L Krinsky, Ph.D.
>> Molecular Graphics and Computation Facility
>> 175 Tan Hall, University of California, Berkeley, CA 94720
>> jamink!=!berkeley.edu, 510-643-0616
>> http://glab.cchem.berkeley.edu>
>>
>
> --
>
> Christopher J. Cramer
> Elmore H. Northey Professor
> University of Minnesota
> Department of Chemistry
> 207 Pleasant St. SE
> Minneapolis, MN 55455-0431
> --------------------------
> Phone: �(612) 624-0859 || FAX: �(612) 626-7541
> Mobile: (952) 297-2575
> email: �cramer*umn.edu
> jabber: �cramer*jabber.umn.edu
> http://pollux.chem.umn.edu/~cramer
> (website includes information about the textbook "Essentials
> � �of Computational Chemistry: �Theories and Models, 2nd Edition")> � �> � �� �>
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/> � �>
>
>
--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink~!~berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu