From owner-chemistry@ccl.net Sat Aug 7 00:24:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim+/-compchem.net" To: CCL Subject: CCL: Gibbs free energy Message-Id: <-42474-100807002243-31593-my73Je21t6eP4e5xM0fHQA..server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001517503b2202db91048d342277 Date: Sat, 7 Aug 2010 05:22:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim]|[compchem.net] --001517503b2202db91048d342277 Content-Type: text/plain; charset=ISO-8859-1 Dear All I am not writing today to answer a question, I am writing just to thank all you. I haven't seen this kind of a highly respectful reply a long time ago. Dr. Jamin's reply was really amazing, respectful, and powerful, I liked his reply. Special thanks for Dr. Charmer and Dr. Jamin Your student; M. Ibrahim On Fri, Aug 6, 2010 at 11:14 PM, Jamin Krinsky jamink ~~ berkeley.edu < owner-chemistry]^[ccl.net> wrote: > > 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 > 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 > >> 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 > >>> 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> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim]^[compchem.net Website: www.compchem.net Fax No.: +20862342601 --001517503b2202db91048d342277 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All
I am not writing today to answer a question, I am writing just= to thank all you.
I haven't seen this kind of a highly respe= ctful reply a long time ago. Dr. Jamin's reply was really amazing,=A0re= spectful, and powerful, I liked his reply.
Special=A0thanks for Dr. Charmer and Dr. Jamin
Your student;=
M. Ibrahim

O= n Fri, Aug 6, 2010 at 11:14 PM, Jamin Krinsky jamink ~~ berkeley.edu <owner-chemistry]^[ccl= .net> wrote:

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<= br> 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 or= iginal
> question.
>
> Within the ideal-gas, rigid-rotator, harmonic-oscillator approximation= , the
> free energy of a molecule "A" is fairly well defined once on= e has
> accomplished a computation of vibrational frequencies for an optimized=
> geometry (I say fairly only because A may have multiple conformers, an= d in
> practice researchers often use only one). Thus, the partition function= s for
> the (i) electronic, (ii) translational, (iii) rotational, and (iv)
> vibrational contributions to the energy are taken as (i) the electroni= c
> state degeneracy (assuming that, at relevant temperatures, excited sta= tes
> are not populated), (ii) dependent only on the molecular weight (parti= cle in
> a box translation, with volume of the box defining the standard state)= ,
> (iii) dependent only on the principal moments of inertia (rigid rotato= r
> 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 tha= t
> these approximations work quite well for most simple gases at low pres= sures
> (where reasonable "ideality" is observed). It is not "d= ouble-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 a= ll
> 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 starti= ng
> partial pressures and/or ending pressure.
>
> As for constraining the A and B molecules to be 50 ang apart, that is<= br> > equivalent to assigning the "reactant" to be an ideal gas th= at is indeed a
> species A - - - - B that is, hmm, shall we call it, bifragmental? Beyo= nd 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 translat= ions
> and rotations of each fragment within the "complex"), and th= e use of the
> harmonic oscillator approximation would be disastrous in such a case.<= br> >
> All of the above being said, certainly one can improve on the "us= ual"
> approximations, e.g., by replacing the harmonic oscillator partition > function with free or hindered rotor partition functions where appropr= iate,
> or by considering anharmonic corrections, or by including centrifugal<= br> > distortion in the rotational partition function, or by including low-e= nergy
> spin-orbit states. Many possibilities. And, there certainly ARE some > ambiguities introduced if we consider attempting to include solvation<= br> > effects by, say, a continuum model (how do the "rotations" o= f a solute in a
> continuum solvent correspond to actual "librations" in a sup= ermolecular
> 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 entropi= es,
>> as the entropy difference associated with the change in moleculari= ty
>> is not accounted for. There has been some talk in the literature a= bout
>> correction factors for this, but I can't seem to remember any<= br> >> 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!=3D!ccl.net> wrote:
>>>
>>> I would first calculate G for each, A, B and C indi= vidually. =A0Then use
>>> the
>>> equation G(rxn)=3DG(c)-(G(a)+G(b)).
>>>
>>> hope that helps
>>>
>>> On Fri, Aug 6, 2010 at 9:37 AM, Wil= liam Flak williamflak++yahoo= .com
>>> <owner-chemistry a ccl.net> wrote:
>>>>
>>>> Sent to CCL by: "William =A0Flak" [williamflak^^= yahoo.com]
>>>> Dear CCL users
>>>> This may be a trivial question, I am not a student but I g= ot confused
>>>> and
>>>> my
>>>> colleagues here say different answers.
>>>> For A + B ---> C, comparing the Gibbs free energy for t= his reaction by:
>>>> G(a)=3D H(a) - TS
>>>> G(b)=3D H(b) - TS
>>>> G(c)=3D H(c) - TS
>>>>
>>>> What is the correct way to calculate G (reaction)?
>>>> =A0G(reaction) =3D G(c) - G(a) - G(b) here A and B calcula= ted in separated
>>>> jobs
>>>> or
>>>> =A0G(reaction) =3D G(c) - G((a)&(b)) here A and B calc= ulated in one single
>>>> job
>>>> and
>>>> separated from each other by 50A
>>>>
>>>> These two methods are different and giving different resul= ts at the same
>>>> level
>>>> of calculation. Counting TS twice in the first equation ma= y be a reason,
>>>> but in
>>>> the second equation accounting rotation and transition deg= rees 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: CHEMI= STRY 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!=3D!berke= ley.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: =A0(612) 624-0859 || FAX: =A0(612) 626-7541
> Mobile: (952) 297-2575
> email: =A0cramer*umn.edu<= /a>
> jabber: =A0cramer*= jabber.umn.edu
> http:= //pollux.chem.umn.edu/~cramer
> (website includes information about the textbook "Essentials
> =A0 =A0of Computational Chemistry: =A0Theories and Models, 2nd Edition= ")> =A0 =A0> =A0 =A0=A0 =A0>
--
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.cc= hem.berkeley.edu






--
=A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Current Address
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0=A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 The University of Manchester,
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa= culty of Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information
=A0 =A0 = =A0 =A0 =A0=A0 Email: m.ibrahim]^[compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Fax No.: +20862342601
--001517503b2202db91048d342277--