De= ar Jiao,

On Tue, 26 Mar 2019 at 04:58, Anyao Jiao 1425= 623121-,-qq.com <owner-chemistry . ccl.net> wrote:

Sent to CCL by: "Anyao=C2=A0 Jiao" [1425623121|qq.com]
Dear all
=C2=A0 =C2=A0 I have a question about the conventional transition state the= ory (TST).For
example, NO+CO-1/2N2+CO2. It is a bimolecular reaction in experiment.

It is also most likely not an elementary reacti= on! I believe for this particular chemistry, you might find a lot of litera= ture in combustion science, where NOx formation has been studied extensivel= y. In fact, almost any real-world NO chemistry is very much affected by CH = radical concentration (Gibaud et al., 10.1016/j.proci.2004.08.006). As a st= arting point, I'll suggest the somewhat dated paper of Williams and Fle= ming (10.1016/0010-2180(94)00146-J), I don't have anything better at ha= nd right now.=C2=A0

=C2=A0

I used TST to
find the rate of this reaction and default it to single molecule reaction. = So how
can I compare the rate between single molecule reaction and=C2=A0 bimolecul= ar reaction?

First, nomenclature: rate = (r) and rate constant (k) are two different things. For elementary reaction= s, the following so-called rate law is generally valid:

r =3D k * [A][B]

where [A] and [B] are conce= ntrations of reactants (or more precisely: activities), and they are raised= to the power of their stoichiometric coefficient (this is only true for el= ementary reactions). Transition state theory calculates k, I believe you= 9;re after r.

For bimolecular reactions, it is per= haps more useful to consider the Eyring equation, which uses the (unitless!= ) equilibrium constant. So for a bimolecular reaction A + B -> [M]^=
=E2=80=A1 -> C + D, it is first assumed that the activated complex= (transition state) [M]^=E2=80=A1 is under steady state condition= s, and its equilibrium constant is:

Keq^=E2=80=
=A1=3D [M]^=E2=80=A1q0 / [A][B]

He= re, q0 is a concentration factor equal to 1 mol/l to balance the units. The= n, apply =CE=94G^=E2=80=A1=3D -RT ln Keq^{=E2=80=A1, and the rate constant can be determined from Eyring equation: k =3D (k=
B T / h) e^(-=CE=94G^=E2=80=A1/RT).}

When you spl= it the Gibbs term into the enthalpy and entropy contributions, and after a = little algebra, you'll see that the entropic contribution scales accord= ing to:

k ~ q^[M]=E2=80=A1/(q^A=q^B)

where q's are the partiti= on functions, and the enthalpic contribution is approximately equal to the = reaction barrier.

Hope that helps,

Peter=

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--000000000000731acc0584f8f042-- From owner-chemistry@ccl.net Tue Mar 26 03:16:00 2019 From: "Norrby, Per-Ola Per-Ola.Norrby**astrazeneca.com" To: CCL Subject: CCL: the conventional transition state theory Message-Id: <-53659-190326012730-26120-y6bUcoASKyx5YNRNjE9ENQ*|*server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Mar 2019 05:27:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby*_*astrazeneca.com] Dear Jiao, Your question requires several answers. First, a bimolecular reaction is accounted for in the Eyring equation, https://en.wikipedia.org/wiki/Eyring_equation . The prefactor together with the activation entropy will give you the activation barrier and from there the reaction rate constant at the standard state (1 atm if you're calculating gas phase reactions; 1 M in solution). Second, you can only apply calculated barriers to exactly defined reactions. The one you propose is not mass balanced (one N to the left, 2 to the right; minus charge on the left, no charge on the right). But if it is a complex reaction consisting of many elementary steps, you must calculate the activation free energy for each step. You then identify the rate limiting TS, which is generally the one with the highest energy. The barrier is calculated as the difference between the free energy of the TS and that of the lowest preceding point on the reaction path (including any potential side reactions creating more stable species). This simple picture can fail if there is a very stable intermediate (much more stable than the products); if so, the reaction will accumulate in the intermediate, and the the rate limiting step is going from that intermediate to the highest subsequent TS. Finally, for each stationary point along the path, you must calculate the energy of the total system. For example, if you have three components, A, B, and C, and they can combine either to generate intermediate AB or AC, then to compare those two steps you must calculate the energies for A+B+C (starting material), AB* + C (TS for combining A and B), AB + C (energy for intermediate AB), AC* + B (TS for combining A and C), and AC + B (intermediate AC). You can only ever compare two states if they have the exact same number and type of atoms and charges. Best regards, Per-Ola -----Original Message----- > From: owner-chemistry+per-ola.norrby==astrazeneca.com(0)ccl.net On Behalf Of Anyao Jiao 1425623121-,-qq.com Sent: den 26 mars 2019 02:30 To: Norrby, Per-Ola Subject: CCL: the conventional transition state theory Sent to CCL by: "Anyao Jiao" [1425623121|qq.com] Dear all I have a question about the conventional transition state theory (TST).For example, NO+CO-1/2N2+CO2.It is a bimolecular reaction in experiment. I used TST to find the rate of this reaction and default it to single molecule reaction. So how can I compare the rate between single molecule reaction and bimolecular reaction?https://clicktime.symantec.com/37p2TGJ9HqrZaiN5eiUbWVL6H2?u=http%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/37p2TGJ9HqrZaiN5eiUbWVL6H2?u=http%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/3QbiBkhdR91vJtdGpFVvWQt6H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsub_unsub.shtml Before posting, check wait time at: https://clicktime.symantec.com/3NZQgQhqPiHwWb4smoW4rLx6H2?u=http%3A%2F%2Fwww.ccl.net Job: https://clicktime.symantec.com/3NLVzCVDsPDKNH8QNULoDFR6H2?u=http%3A%2F%2Fwww.ccl.net%2Fjobs Conferences: https://clicktime.symantec.com/3GMQ9FTQGcAEzcue4BYmwGp6H2?u=http%3A%2F%2Fserver.ccl.net%2Fchemistry%2Fannouncements%2Fconferences%2F Search Messages: https://clicktime.symantec.com/39sNLk2pc9XczVNGY6LooUf6H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsearchccl%2Findex.shtmlhttps://clicktime.symantec.com/38VLux4mFxdtcmXPVtZAe1j6H2?u=http%3A%2F%2Fwww.ccl.net%2Fspammers.txt RTFI: https://clicktime.symantec.com/32pEhpEbpApECWSenA1xJcE6H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Faboutccl%2Finstructions%2F ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. From owner-chemistry@ccl.net Tue Mar 26 15:47:01 2019 From: "Mo Fateh mo.fateh ~~ yahoo.com" To: CCL Subject: CCL:G: Gaussian 16, the best functional for OPT organic molecules Message-Id: <-53660-190326153014-6795-AgQ0ppvzdKs0CIxSbpHmjQ[A]server.ccl.net> X-Original-From: "Mo Fateh" Date: Tue, 26 Mar 2019 15:30:13 -0400 Sent to CCL by: "Mo Fateh" [mo.fateh : yahoo.com] Dear CClers, I want to optimize organic molecules under the effect of electric field. I use Gaussian 16, and I do not like to use B3LYP anymore. Please suggest any new functional or even old that implemented in Gaussian 16 and give good results in the presence of electric field. Best regards, Mo Fateh From owner-chemistry@ccl.net Tue Mar 26 19:14:01 2019 From: "Simmie, John john.simmie!A!nuigalway.ie" To: CCL Subject: CCL: TST of NO+CO Message-Id: <-53661-190326060245-24448-6ty23C/ez9ysQ4yY9zRPgw:server.ccl.net> X-Original-From: "Simmie, John" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DB7PR01MB5340223DC50A3042AFA5DF06945F0DB7PR01MB5340eurp_" Date: Tue, 26 Mar 2019 10:02:37 +0000 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie]_[nuigalway.ie] --_000_DB7PR01MB5340223DC50A3042AFA5DF06945F0DB7PR01MB5340eurp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Jiao: The well known reaction mechanism GRI-MECH 3.0 contains data for the rever= se reaction: N + CO2 =3D=3D> NO + CO (I think this reaction is what you were trying to = show? All neutral species ... no charged species involved) And gives an A-factor of 3.0E+12 and activation energy of 11.3 kcal/mol So via the equilibrium constant you can back calculate the rate constant fo= r the bimolecular reaction There is no unimolecular reaction at all involved here. "GRI-Mech 3.0 is an optimized mechanism designed to model natural gas combu= stion, including NO formation and reburn chemistry." If you want to compute the rate constant via TS theory yourself then I reco= mmend using MultiWell Program Suite which is very straightforward Best, Emeritus Professor John M. Simmie School of Chemistry::National University of Ireland, Galway Ireland H91 TK33 Tel. +353-91-492451, +353-86-805-9948 --_000_DB7PR01MB5340223DC50A3042AFA5DF06945F0DB7PR01MB5340eurp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Jiao:

The well known reaction mechanism GRI-MECH 3.0 contains data for the = reverse reaction:

N + CO2 =3D=3D> NO + CO (I think this reaction is wha= t you were trying to show? All neutral species … no charged species i= nvolved)

And gives an A-factor of 3.0E+12 and activation energy of 11.3 kca= l/mol

So via the equilibrium constant you can back calculate the rate consta= nt for the bimolecular reaction

There is no unimolecular reaction at all involved here.

&nbs= p;

“GRI-Mech 3.0 is an optimized mechanism designed to model natura= l gas combustion, including NO formation and reburn chemistry.”

&nbs= p;

If you want to compute the rate constant via TS theory yourself then I= recommend using MultiWell Program Suite which is very straightforward

&nbs= p;

Best,

&nbs= p;

&nbs= p; &= nbsp; Emeritus Professor John M. Simmie

Scho= ol of Chemistry::National University of Ireland, Galway

&nbs= p; &= nbsp; &nbs= p; Ireland H91 TK33<= /font>

&nbs= p; = Tel. +353-91-492451, +353-86-805-9948

&nbs= p;

--_000_DB7PR01MB5340223DC50A3042AFA5DF06945F0DB7PR01MB5340eurp_-- From owner-chemistry@ccl.net Tue Mar 26 19:48:00 2019 From: "Robert Molt r.molt.chemical.physics!A!gmail.com" To: CCL Subject: CCL:G: Gaussian 16, the best functional for OPT organic molecules Message-Id: <-53662-190326194203-22133-LMh7cOshsfzOtwrUoSnr0w#server.ccl.net> X-Original-From: Robert Molt Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 26 Mar 2019 19:41:55 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics!^!gmail.com] Do a literature search for a review on DFT functionals. Read a review article or two. There are dozens written by Grimme, Mark Gordon, Truhlar, etc. The worst thing you can do is rely on one particular voice or just a few people. Science is not a popularity contest; look at the evidence. On 3/26/19 3:30 PM, Mo Fateh mo.fateh ~~ yahoo.com wrote: > Sent to CCL by: "Mo Fateh" [mo.fateh : yahoo.com] > Dear CClers, > > I want to optimize organic molecules under the effect of electric field. I > use Gaussian 16, and I do not like to use B3LYP anymore. Please suggest any > new functional or even old that implemented in Gaussian 16 and give good > results in the presence of electric field. > > Best regards, > Mo Fateh> > -- Dr. Robert Molt Jr. r.molt.chemical.physics/./gmail.com From owner-chemistry@ccl.net Tue Mar 26 23:07:00 2019 From: "Geoffrey Hutchison geoff.hutchison!A!gmail.com" To: CCL Subject: CCL: Gaussian 16, the best functional for OPT organic molecules Message-Id: <-53663-190326230524-26776-NM+zviJIZc73rzhPZw5xfg..server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 26 Mar 2019 23:05:16 -0400 Mime-Version: 1.0 (Mac OS X Mail 12.2 $3445.102.3$) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison#,#gmail.com] > Do a literature search for a review on DFT functionals. Read a review article or two. There are dozens written by Grimme, Mark Gordon, Truhlar, etc. This is critical advice. Beyond this, make sure you're using good dispersion correction (e.g., D3BJ, VV10, etc.), which are typically mentioned in recent critical reviews. You mention effects in response to an electric field. In this case, besides the usual review articles mentioned above, you should look at the effects on polarizability (i.e., does a particular functional correctly model changes in electron density with your electric field). Hait and Head-Gordon had a recent assessment: Phys. Chem. Chem. Phys., 2018, 20, 19800-19810 Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh-$-pitt.edu twitter: -$-ghutchis web: https://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Tue Mar 26 23:42:00 2019 From: "Yu Zhai yuzhai:mail.huiligroup.org" To: CCL Subject: CCL:G: Gaussian 16, the best functional for OPT organic molecules Message-Id: <-53664-190326222351-24313-odpdaMwdZ+BJMNS9pflKNA%server.ccl.net> X-Original-From: Yu Zhai Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 27 Mar 2019 10:23:34 +0800 MIME-Version: 1.0 Sent to CCL by: Yu Zhai [yuzhai{:}mail.huiligroup.org] Dear Mo, Hello! I am just curious why you do not like B3LYP. It is cute. Generally, there is NO such suggestion can be made in what functional you should use. Your system was not clearly stated. Basically, we choose functional by considering what system you are going to study, what accuracy you like, and even what properties you are estimating. Then you can look for some published papers for some general suggestions. However, they could be WRONG---a lot of researchers just use some most commonly seen functionals/basis sets to finish the job. About the presence of electric fields, you may find that in QM/MM method, the environment effects the QM part somehow by electrostatic interaction. It means the QM calculation is done with electric field presenting! See, https://doi.org/10.1007%2Fs00214-006-0143-z . FYI, a lot of such calculations are performed with B3LYP for the QM part. However, when people study some solids in electric field, they prefer using PBE series. For your organic system, beside B3LYP, you may want to use Minnesota series (M06, M15, etc.), or some other hybrid functionals, even some double hybrid ones (read the papers of these functionals first, by the way. There are some interesting variants). But I cannot guarantee that they work fine. In conclusion, I do suggest benchmarking your functional first before the massive computation. Cheers, Yu Zhai On 3/27/2019 03:30, Mo Fateh mo.fateh ~~ yahoo.com wrote: > Sent to CCL by: "Mo Fateh" [mo.fateh : yahoo.com] > Dear CClers, > > I want to optimize organic molecules under the effect of electric field. I > use Gaussian 16, and I do not like to use B3LYP anymore. Please suggest any > new functional or even old that implemented in Gaussian 16 and give good > results in the presence of electric field. > > Best regards, > Mo Fateh> >