From owner-chemistry@ccl.net Tue May 15 00:31:00 2018 From: "fede green nicogreen6-$-gmail.com" To: CCL Subject: CCL: Ignorant question Message-Id: <-53300-180515000155-18442-gDBwKSJ/+K4BQaT3ehQnYg(!)server.ccl.net> X-Original-From: "fede green" Date: Tue, 15 May 2018 00:01:53 -0400 Sent to CCL by: "fede green" [nicogreen6|-|gmail.com] Dear all, I am quite new in this and I have an ignorant question: I am studying a competitive mechanism in which I have a path with the first TS lower in energy (around 20kcal) giving an intermediate 8 kcal higher. The rest of the path of this lower TS is mostly uphill until the product. The competing path, has the TS 20kcal above, but after that TS the intermediate has a relative energy of -25kcal/mol. Also goes uphill but slower. One thing that should be noted that the biggest barrier (relative between TS and the corresponding stable intermediate) is on the 2nd path, 2kcal higher than in the first. Which is supposed to be the preferred path? I hope it is understandable (apologize for my English and the lack of "correctness" in the terms Regards Fede From owner-chemistry@ccl.net Tue May 15 02:45:00 2018 From: "Per-Ola Norrby per-ola.norrby+/-astrazeneca.com" To: CCL Subject: CCL: Ignorant question Message-Id: <-53301-180515024322-29043-oZbn+92gvY/JnVCBy2e6ag:server.ccl.net> X-Original-From: "Per-Ola Norrby" Date: Tue, 15 May 2018 02:43:19 -0400 Sent to CCL by: "Per-Ola Norrby" [per-ola.norrby-x-astrazeneca.com] Dear Fede, Each barrier should be calculated from the lowest preceding point, even if there are other (lower) barriers in between. This is true even if the lower point is on a side path. Both paths you have calculated should have their highest points related to the same species (possibly the starting material, unless you have a lower point on one of the paths). From this you can see that you should take the highest points on each path and compare them to each other. The lower of them will be the preferred path. If you want to read more, look up "Curtin-Hammett", the kinetics were worked out early last century. If you can access the book below, I wrote half a chapter on this a few years back: "Modeling in Homogeneous Catalysis: a Tutorial" Eric Clot and Per-Ola Norrby, in Innovative Catalysis in Organic Synthesis: Oxidation, Hydrogenation, and C-X Bond Forming Reactions, Ed: P. Andersson, Wiley-VCH, 2012, 167-191 http://dx.doi.org/10.1002/9783527646586.ch8 For a more recent method that gives the same result, look at the "energy span" model from Kozuch and Shaik. Kind regards, Per-Ola From owner-chemistry@ccl.net Tue May 15 12:17:01 2018 From: "Sebastian seb.kozuch^gmail.com" To: CCL Subject: CCL: Ignorant question Message-Id: <-53302-180515022823-27866-dzJt3c2fwOsfLWm6SuBJdw.:.server.ccl.net> X-Original-From: Sebastian Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=utf-8 Date: Tue, 15 May 2018 09:28:27 +0300 MIME-Version: 1.0 Sent to CCL by: Sebastian [seb.kozuch||gmail.com] Dear Fede,
It is complicated to give an answer to your question without looking at the whole energy profile. However, with the energy profile it is easy to answer.
I am sorry for the self-promotion, but if you look at the energy span model it is typically straightforward to tell which mechanism is faster, and what would be the rate. Although this model is for catalysis, it can be easily adapted for stoichiometric reactions as well (I don't know to which family your reaction corresponds to). You can read about this in:
http://dx.doi.org/10.1021/acscatal.5b00694
http://dx.doi.org/10.1002/wcms.1100
http://pubs.acs.org/doi/abs/10.1021/ar1000956

Hope this helps,
Sebastian

On 15/05/2018 7:01, fede green nicogreen6-$-gmail.com wrote:

Sent to CCL by: "fede  green" [nicogreen6|-|gmail.com]
Dear all,
I am quite new in this and I have an ignorant question:

I am studying a competitive mechanism in which I have a path with the first TS lower in energy (around 
20kcal) giving an intermediate 8 kcal higher. The rest of the path of this lower TS is mostly uphill until the 
product.
The competing path, has the TS 20kcal above, but after that TS the intermediate has a relative energy of 
-25kcal/mol. Also goes uphill but slower.
One thing that should be noted that the biggest barrier (relative between TS and the corresponding 
stable intermediate) is on the 2nd path, 2kcal higher than in the first.

Which is supposed to be the preferred path?

I hope it is understandable (apologize for my English and the lack of "correctness" in the terms

Regards

FedeE-mail to subscribers: CHEMISTRY|ccl.net or use:
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-- 
═════════════════════════════════════
          Sebastian Kozuch
═════════════════════════════════════
       Department of Chemistry
 Ben-Gurion University of the Negev 
          Beer Sheva, Israel
           kozuch|bgu.ac.il
    http://www.bgu.ac.il/~kozuch
═════════════════════════════════════

From owner-chemistry@ccl.net Tue May 15 12:52:01 2018 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor~!~fluor.quimica.uniovi.es" To: CCL Subject: CCL: Ignorant question Message-Id: <-53303-180515113946-2485-Ot4xO7j/+y6+HBSemw34RQ^^^server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 15 May 2018 17:39:34 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor!^!fluor.quimica.uniovi.es] * fede green nicogreen6-$-gmail.com [2018-05-15 00:01:53 -0400]: > > Sent to CCL by: "fede green" [nicogreen6|-|gmail.com] > Dear all, > I am quite new in this and I have an ignorant question: > > I am studying a competitive mechanism in which I have a path with the first TS lower in energy (around > 20kcal) giving an intermediate 8 kcal higher. The rest of the path of this lower TS is mostly uphill until the > product. > The competing path, has the TS 20kcal above, but after that TS the intermediate has a relative energy of > -25kcal/mol. Also goes uphill but slower. > One thing that should be noted that the biggest barrier (relative between TS and the corresponding > stable intermediate) is on the 2nd path, 2kcal higher than in the first. > > Which is supposed to be the preferred path? > > I hope it is understandable (apologize for my English and the lack of "correctness" in the terms Fede, Not only the energy along the path is important, the geometry plays also an important role in the preexponential factor. Which is your mother tongue?, if you let me ask. Best regards, V�ctor Lua�a -- . . "Never let your sense of morals prevent you from / `' \ doing what is right." /(o)(o)\ -- Salvor Hardin, "Foundation" /`. \/ .'\ / '`'` \ "Freedom!, freedom!, freedom! After that put whatever | \'`'`/ | term you like" | |'`'`| | --Largo Caballero (socialist, spanish president in the exile, \/`'`'`'\/ shortly before dying) ==(((==)))===================================+=========================== ! Dr.V�ctor Lua�a, in silico chemist & prof. ! A person is slave of his words ! Departamento de Qu�mica F�sica y Anal�tica ! and owner of his silences. ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! What has been seen cannot ! phone: +34-984080927 fax: +34-985103125 ! be unseen, �are you sure? +--------------------------------------------+ GroupPage: Articles: git-hub: ORCID: 0000-0003-4585-4627; RID: H-2045-2015 From owner-chemistry@ccl.net Tue May 15 14:46:00 2018 From: "Andrew Rosen rosen]![u.northwestern.edu" To: CCL Subject: CCL: Ignorant question Message-Id: <-53304-180515144406-5585-m839QZPlYWvEolF0r2bfLQ|-|server.ccl.net> X-Original-From: Andrew Rosen Content-Type: multipart/alternative; boundary="00000000000047761d056c42fc0c" Date: Tue, 15 May 2018 13:43:48 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Rosen [rosen .. u.northwestern.edu] --00000000000047761d056c42fc0c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Fede, Depending on what you are defining as "preferred path", the answer may vary. Assuming you are interested in which pathway has the faster rate, your best bet is to create a microkinetic model for both mechanisms using the barriers for each step (and the pre-exponential factors computed from statistical thermodynamics). Otherwise, it's hard to tell in advance which of the two pathways is favorable (at least based on the information given). You may also be interested in the concept of the "degree of rate control", which identifies the rate-controlling transition states and/or intermediates in a mechanism (https://pubs.acs.org/doi/abs/10.1021/ja900009= 7). This could provide additional insight into the critical steps. Andrew On Tue, May 15, 2018 at 1:24 PM V=C3=ADctor Lua=C3=B1a Cabal victor~!~ fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor!^= ! > fluor.quimica.uniovi.es] > * fede green nicogreen6-$-gmail.com > [2018-05-15 00:01:53 -0400]: > > > > Sent to CCL by: "fede green" [nicogreen6|-|gmail.com] > > Dear all, > > I am quite new in this and I have an ignorant question: > > > > I am studying a competitive mechanism in which I have a path with the > first TS lower in energy (around > > 20kcal) giving an intermediate 8 kcal higher. The rest of the path of > this lower TS is mostly uphill until the > > product. > > The competing path, has the TS 20kcal above, but after that TS the > intermediate has a relative energy of > > -25kcal/mol. Also goes uphill but slower. > > One thing that should be noted that the biggest barrier (relative > between TS and the corresponding > > stable intermediate) is on the 2nd path, 2kcal higher than in the first= . > > > > Which is supposed to be the preferred path? > > > > I hope it is understandable (apologize for my English and the lack of > "correctness" in the terms > > Fede, > > Not only the energy along the path is important, the geometry plays also > an important role in the preexponential factor. > > Which is your mother tongue?, if you let me ask. > > Best regards, > V=C3=ADctor Lua=C3=B1a > -- > . . "Never let your sense of morals prevent you from > / `' \ doing what is right." > /(o)(o)\ -- Salvor Hardin, "Foundation" > /`. \/ .'\ > / '`'` \ "Freedom!, freedom!, freedom! After that put whatever > | \'`'`/ | term you like" > | |'`'`| | --Largo Caballero (socialist, spanish president in the exil= e, > \/`'`'`'\/ shortly before dying) > =3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! A person is slav= e of his > words > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! and owner o= f his silences. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: ! What has been seen cannot > ! phone: +34-984080927 <+34%20984%2008%2009%2027> fax: +34-985103125 > <+34%20985%2010%2031%2025> ! be unseen, =C2=BFare you sure? > +--------------------------------------------+ > GroupPage: > Articles: > git-hub: > ORCID: 0000-0003-4585-4627; RID: H-2045-2015 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --00000000000047761d056c42fc0c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Fede,

Depending on what you are definin= g as "preferred path", the answer may vary. Assuming you are inte= rested in which pathway has the faster rate, your best bet is to create a m= icrokinetic model for both mechanisms using the barriers for each step (and= the pre-exponential factors computed from statistical thermodynamics). Oth= erwise, it's hard to tell in advance which of the two pathways is favor= able (at least based on the information given). You may also be interested = in the concept of the "degree of rate control", which identifies = the rate-controlling transition states and/or intermediates in a mechanism = (https://pubs.ac= s.org/doi/abs/10.1021/ja9000097). This could provide additional insight= into the critical steps.

Andrew

On Tue, May 15, 2018 at 1:24 PM V= =C3=ADctor Lua=C3=B1a Cabal victor~!~fluor.quimica.uniovi.es <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor!^!<= a href=3D"http://fluor.quimica.uniovi.es" rel=3D"noreferrer" target=3D"_bla= nk">fluor.quimica.uniovi.es]
* fede green nicogreen6-$-gmail.com <owner-chemistry||ccl.net> [2018-05-15 00:01:= 53 -0400]:
>
> Sent to CCL by: "fede=C2=A0 green" [nicogreen6|-|gmail.com]
> Dear all,
> I am quite new in this and I have an ignorant question:
>
> I am studying a competitive mechanism in which I have a path with the = first TS lower in energy (around
> 20kcal) giving an intermediate 8 kcal higher. The rest of the path of = this lower TS is mostly uphill until the
> product.
> The competing path, has the TS 20kcal above, but after that TS the int= ermediate has a relative energy of
> -25kcal/mol. Also goes uphill but slower.
> One thing that should be noted that the biggest barrier (relative betw= een TS and the corresponding
> stable intermediate) is on the 2nd path, 2kcal higher than in the firs= t.
>
> Which is supposed to be the preferred path?
>
> I hope it is understandable (apologize for my English and the lack of = "correctness" in the terms

Fede,

Not only the energy along the path is important, the geometry plays also an important role in the preexponential factor.

Which is your mother tongue?, if you let me ask.

Best regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0V=C3=ADctor Lua=C3=B1a
--
=C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "Never let your sense of morals p= revent you from
=C2=A0 =C2=A0/ `' \=C2=A0 =C2=A0doing what is right."
=C2=A0 /(o)(o)\=C2=A0 -- Salvor Hardin, "Foundation"
=C2=A0/`. \/ .'\=C2=A0
/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ "Freedom!, freedom!, freedom!= After that put whatever
|=C2=A0 \'`'`/=C2=A0 | term you like"
|=C2=A0 |'`'`|=C2=A0 |=C2=A0 --Largo Caballero (socialist, spanish = president in the exile,
=C2=A0\/`'`'`'\/=C2=A0 =C2=A0shortly before dying)
=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! A person is sl= ave of his words
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! and owner of = his silences.
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:=C2=A0 <victor||fluor.quimica.uniovi.es>=C2=A0 ! W= hat has been seen cannot
! phone: +34-984080927=C2=A0 =C2=A0 fax: +34-985103125 ! be unseen, =C2=BFare you sure?
+--------------------------------------------+
=C2=A0GroupPage: <http://azufre.quimica.uniovi.es/>
=C2=A0Articles:=C2=A0 <http://= scholar.google.com/citations?user=3DIbl1BWAAAAAJ&hl=3Des>
=C2=A0git-hub:=C2=A0 =C2=A0<https://github.com/aoterodelaroza>
=C2=A0ORCID: 0000-0003-4585-4627; RID: H-2045-2015

-=3D This is automatically added to each message by the mailing script =3D-=
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