From owner-chemistry@ccl.net Sun May 27 14:49:01 2018 From: "Sebastian seb.kozuch^^^gmail.com" To: CCL Subject: CCL: RateDetermining State Message-Id: <-53323-180527024513-24778-n/XrxpcDMUv96OIXyET2mg|,|server.ccl.net> X-Original-From: Sebastian Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=utf-8 Date: Sun, 27 May 2018 09:45:28 +0300 MIME-Version: 1.0 Sent to CCL by: Sebastian [seb.kozuch(_)gmail.com] Dear Robert,
I am sorry to disagree, but I don't think that RDStep and RDState are the same concept. Actually I believe that the former is very misleading. You see, when people speak about the RDStep, they really speak about an elementary step (or a couple of connected elementary steps). For instance, you can say that the oxidative addition is the RDStep in a cross coupling reaction, or that the oxygen chemisorption is the RDStep in the CO oxidation in heterogeneous catalysis. This is incorrect in many (if not in most) situations.
I apologize for the auto-citations (and the mildly arrogant tone), but I cannot write all the explanations here. I will just summarize them.
If you can check this concept article (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137) you will see that defining the RDStep is extremely problematic. Most definitions are actually wrong, and 90% (a conservative number) of the chemical textbooks really fail in trying to explain what is a RDStep. The best definition I could find is the one that appears in IUPAC's Gold book (http://goldbook.iupac.org/html/R/R05139.html). They define the "control factor", which is very similar to the "degree of rate control" by Campbell (https://pubs.acs.org/doi/10.1021/acscatal.7b00115). From my perspective those definitions are correct, but are actually defining a rate-determining transition state. Still, they are missing half of the kinetic information, i.e. the rate-determining intermediate (defined by Campbell in the "thermodynamic degree of rate control").  This intermediate is sometimes called the MARI (most abundant reaction intermediate) or the resting state. Without both states (RD-TS and RD-Int) you cannot define the rate of the reaction, and therefore the RDStep concept fails. What makes much more sense is to define a rate-determining zone (from the RD-Int to the RD-TS), an almost forgotten concept by Yagisawa (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1136877/, see also https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527678211.ch9#), which helps understand which reactants and products affect the kinetics of the reaction.

Best,
Sebastian

On 26/05/2018 23:30, Robert Molt r.molt.chemical.physics|a|gmail.com wrote:

In short, "rate-determining step" is a shorthand way of saying that which is more explicitly and carefully defined in a "rate-determining state." The former is intuitive and clear in its meaning, thinking in terms of a two-state system; the latter considers the problem from the perspective of ensembles of states which lead to a given TS. They are not different except when a two-state model is not applicable to describe the kinetics.


On 5/24/18 2:09 AM, Norrby, Per-Ola Per-Ola.Norrby-x-astrazeneca.com wrote:

So the concept of rate determining state has been around for about a decade now, it came out of the same work as the energetic span model, from Sebastian Kozuch and Saison Shaik. It’s valid, I’m not contesting that, but there isn’t really a conflict. The “rate determining step” is also a valid concept, you just have to define a “step” as done in kinetics, and apply the Curtin-Hammett principle. In short, if a “step” is considered to go to a transition state from the lowest preceding point, not the closest minimum, then the models work out the same. A simple trick really, you calculate the barrier associated with each transition state by looking back to the lowest preceding point that you can reach without passing a higher barrier. In catalysis, that lowest preceding point could be the resting state, another very useful concept that has also been considered dead, but which is handy when trying to predict what will be observable.

 

Also note that the lowest preceding point does not have to lie on the productive reaction path, it can easily be a side path, a thermodynamic dump that just slows the overall kinetics.

 

I haven’t found an article that summarizes this view. It underlies how many of us handled potential energy surfaces decades back, but I never saw it stated explicitly, it was just handed down as essential knowledge in computational groups with expertise in kinetics. I did write a summary in a book chapter a while back, can be found here: http://dx.doi.org/10.1002/9783527646586.ch8

 

/Per-Ola

 

Per-Ola Norrby

Principal Scientist, Computational Pharmaceutics

Pharmaceutical Sciences, AstraZeneca-Gothenburg

 

 

 

From: owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net [mailto:owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net] On Behalf Of Andrew Rosen rosen__u.northwestern.edu
Sent: den 24 maj 2018 05:34
To: Norrby, Per-Ola <Per-Ola.Norrby===astrazeneca.com>
Subject: CCL: RateDetermining State

 

Anyao,

 

I refer you to the following two papers:

1) "Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates" (https://pubs.acs.org/doi/abs/10.1021/ja9000097)

2) "The Rate‐Determining Step is Dead. Long Live the Rate‐Determining State!" (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137)

 

From a detailed mechanistic point of view, it is often much more insightful to talk about about a rate-determining state (either transition state or intermediate) than a rate-determining step. The first paper describes the widely used definition of a rate-controlling state and how to compute it. The second paper contains a few short examples of how the rate-determining state differs from the rate-determining step.

 

On Wed, May 23, 2018 at 10:19 PM Anyao Jiao 1425623121(_)qq.com <owner-chemistry*ccl.net> wrote:


Sent to CCL by: "Anyao  Jiao" [1425623121^qq.com]
Dear All,
  I have a simple question regarding RateDetermining State. My reviewers
suggest me to use RateDetermining State rather than Rate-Determining Step
owning to its inaccuracy. Is that right? If we use the Canonical variational
transition-state theory method, how do you calculate the reaction rate of the
RateDetermining State ?     
   Sincerely

   Anyao Jiao




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-- 
Dr. Robert Molt Jr.
r.molt.chemical.physics===gmail.com

-- 
═════════════════════════════════════
          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 Sun May 27 16:53:00 2018 From: "Robert Molt r.molt.chemical.physics]*[gmail.com" To: CCL Subject: CCL: RateDetermining State Message-Id: <-53324-180527163152-2807-tMaeQ+eMC+ua/6Ci1lVwoA#,#server.ccl.net> X-Original-From: Robert Molt Content-Language: en-US Content-Type: multipart/alternative; boundary="------------E674ECBB774BEEF5C9F57C6F" Date: Sun, 27 May 2018 16:30:54 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics{=}gmail.com] This is a multi-part message in MIME format. --------------E674ECBB774BEEF5C9F57C6F Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit OK Sebastian. You are the originator of the concept of rate-limiting.  No one ever had the idea that there is a "slowest part" in a process before your work. The idea of a rate-determining step in no way relates to a rate-determining state. On 5/27/18 2:45 AM, Sebastian seb.kozuch^^^gmail.com wrote: > Sent to CCL by: Sebastian [seb.kozuch(_)gmail.com] Dear Robert, > I am sorry to disagree, but I don't think that RDStep and RDState are > the same concept. Actually I believe that the former is very > misleading. You see, when people speak about the RDStep, they really > speak about an elementary step (or a couple of connected elementary > steps). For instance, you can say that the oxidative addition is the > RDStep in a cross coupling reaction, or that the oxygen chemisorption > is the RDStep in the CO oxidation in heterogeneous catalysis. This is > incorrect in many (if not in most) situations. > I apologize for the auto-citations (and the mildly arrogant tone), but > I cannot write all the explanations here. I will just summarize them. > If you can check this concept article > (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137) you > will see that defining the RDStep is extremely problematic. Most > definitions are actually wrong, and 90% (a conservative number) of the > chemical textbooks really fail in trying to explain what is a RDStep. > The best definition I could find is the one that appears in IUPAC's > Gold book (http://goldbook.iupac.org/html/R/R05139.html). They define > the "control factor", which is very similar to the "degree of rate > control" by Campbell > (https://pubs.acs.org/doi/10.1021/acscatal.7b00115). From my > perspective those definitions are correct, but are actually defining a > rate-determining transition state. Still, they are missing half of the > kinetic information, i.e. the rate-determining intermediate (defined > by Campbell in the "thermodynamic degree of rate control").  This > intermediate is sometimes called the MARI (most abundant reaction > intermediate) or the resting state. Without both states (RD-TS and > RD-Int) you cannot define the rate of the reaction, and therefore the > RDStep concept fails. What makes much more sense is to define a > rate-determining zone (from the RD-Int to the RD-TS), an almost > forgotten concept by Yagisawa > (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1136877/, see also > https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527678211.ch9#), > which helps understand which reactants and products affect the > kinetics of the reaction. > > Best, > Sebastian > > On 26/05/2018 23:30, Robert Molt r.molt.chemical.physics|a|gmail.com > wrote: >> >> In short, "rate-determining step" is a shorthand way of saying that >> which is more explicitly and carefully defined in a "rate-determining >> state." The former is intuitive and clear in its meaning, thinking in >> terms of a two-state system; the latter considers the problem from >> the perspective of ensembles of states which lead to a given TS. They >> are not different except when a two-state model is not applicable to >> describe the kinetics. >> >> >> On 5/24/18 2:09 AM, Norrby, Per-Ola Per-Ola.Norrby-x-astrazeneca.com >> wrote: >>> >>> So the concept of rate determining state has been around for about a >>> decade now, it came out of the same work as the energetic span >>> model, from Sebastian Kozuch and Saison Shaik. It’s valid, I’m not >>> contesting that, but there isn’t really a conflict. The “rate >>> determining step” is also a valid concept, you just have to define a >>> “step” as done in kinetics, and apply the Curtin-Hammett principle. >>> In short, if a “step” is considered to go to a transition state from >>> the lowest preceding point, not the closest minimum, then the models >>> work out the same. A simple trick really, you calculate the barrier >>> associated with each transition state by looking back to the lowest >>> preceding point that you can reach without passing a higher barrier. >>> In catalysis, that lowest preceding point could be the resting >>> state, another very useful concept that has also been considered >>> dead, but which is handy when trying to predict what will be observable. >>> >>> Also note that the lowest preceding point does not have to lie on >>> the productive reaction path, it can easily be a side path, a >>> thermodynamic dump that just slows the overall kinetics. >>> >>> I haven’t found an article that summarizes this view. It underlies >>> how many of us handled potential energy surfaces decades back, but I >>> never saw it stated explicitly, it was just handed down as essential >>> knowledge in computational groups with expertise in kinetics. I did >>> write a summary in a book chapter a while back, can be found here: >>> http://dx.doi.org/10.1002/9783527646586.ch8 >>> >>> /Per-Ola >>> >>> Per-Ola Norrby >>> >>> Principal Scientist, Computational Pharmaceutics >>> >>> Pharmaceutical Sciences, AstraZeneca-Gothenburg >>> >>> *From:* owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net >>> [mailto:owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net] >>> *On Behalf Of *Andrew Rosen rosen__u.northwestern.edu >>> *Sent:* den 24 maj 2018 05:34 >>> *To:* Norrby, Per-Ola >>> *Subject:* CCL: RateDetermining State >>> >>> Anyao, >>> >>> I refer you to the following two papers: >>> >>> 1) "Degree of Rate Control: How Much the Energies of Intermediates >>> and Transition States Control Rates" >>> (https://pubs.acs.org/doi/abs/10.1021/ja9000097 >>> ) >>> >>> 2) "The Rate‐Determining Step is Dead. Long Live the >>> Rate‐Determining State!" >>> (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137 >>> ) >>> >>> From a detailed mechanistic point of view, it is often much more >>> insightful to talk about about a rate-determining state (either >>> transition state or intermediate) than a rate-determining step. The >>> first paper describes the widely used definition of a >>> rate-controlling state and how to compute it. The second paper >>> contains a few short examples of how the rate-determining state >>> differs from the rate-determining step. >>> >>> On Wed, May 23, 2018 at 10:19 PM Anyao Jiao 1425623121(_)qq.com >>> >>> > wrote: >>> >>> >>> Sent to CCL by: "Anyao  Jiao" [1425623121^qq.com >>> ] >>> Dear All, >>>   I have a simple question regarding RateDetermining State. My >>> reviewers >>> suggest me to use RateDetermining State rather than >>> Rate-Determining Step >>> owning to its inaccuracy. Is that right? If we use the Canonical >>> variational >>> transition-state theory method, how do you calculate the >>> reaction rate of the >>> RateDetermining State ? >>>    Sincerely >>> >>>    Anyao Jiao >>> >>> >>> >>> >>> E-mail to subscribers: CHEMISTRY*ccl.net >>> or use: >>> >>> >>> E-mail to administrators: >>> CHEMISTRY-REQUEST*ccl.net >>> or use >>> >>>
>> >>> >>> Before posting, check wait time at: >>> http://www.ccl.net >>> >> >>> >>> Conferences: >>> http://server.ccl.net/chemistry/announcements/conferences/ >>> >>> >>> Search Messages: >>> http://www.ccl.net/chemistry/searchccl/index.shtml >>> >>>
>> >>> >>> RTFI: >>> http://www.ccl.net/chemistry/aboutccl/instructions/ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> *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. >>> >> >> -- >> Dr. Robert Molt Jr. >> r.molt.chemical.physics===gmail.com > > -- > ═════════════════════════════════════ > Sebastian Kozuch > ═════════════════════════════════════ > Department of Chemistry > Ben-Gurion University of the Negev > Beer Sheva, Israel > kozuch-.-bgu.ac.il > http://www.bgu.ac.il/~kozuch > ═════════════════════════════════════ > -= 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 *o* sign. You can > alsoE-mail to > subscribers: CHEMISTRY*o*ccl.net or use:E-mail to > administrators: CHEMISTRY-REQUEST*o*ccl.net or useBefore posting, check > wait time at: http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your > mail bounces from CCL with 5.7.1 error, check:RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ -- Dr. Robert Molt Jr. r.molt.chemical.physics*o*gmail.com --------------E674ECBB774BEEF5C9F57C6F Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

OK Sebastian. You are the originator of the concept of rate-limiting.  No one ever had the idea that there is a "slowest part" in a process before your work. The idea of a rate-determining step in no way relates to a rate-determining state.


On 5/27/18 2:45 AM, Sebastian seb.kozuch^^^gmail.com wrote:
Sent to CCL by: Sebastian [seb.kozuch(_)gmail.com] Dear Robert,
I am sorry to disagree, but I don't think that RDStep and RDState are the same concept. Actually I believe that the former is very misleading. You see, when people speak about the RDStep, they really speak about an elementary step (or a couple of connected elementary steps). For instance, you can say that the oxidative addition is the RDStep in a cross coupling reaction, or that the oxygen chemisorption is the RDStep in the CO oxidation in heterogeneous catalysis. This is incorrect in many (if not in most) situations.
I apologize for the auto-citations (and the mildly arrogant tone), but I cannot write all the explanations here. I will just summarize them.
If you can check this concept article (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137) you will see that defining the RDStep is extremely problematic. Most definitions are actually wrong, and 90% (a conservative number) of the chemical textbooks really fail in trying to explain what is a RDStep. The best definition I could find is the one that appears in IUPAC's Gold book (http://goldbook.iupac.org/html/R/R05139.html). They define the "control factor", which is very similar to the "degree of rate control" by Campbell (https://pubs.acs.org/doi/10.1021/acscatal.7b00115). From my perspective those definitions are correct, but are actually defining a rate-determining transition state. Still, they are missing half of the kinetic information, i.e. the rate-determining intermediate (defined by Campbell in the "thermodynamic degree of rate control").  This intermediate is sometimes called the MARI (most abundant reaction intermediate) or the resting state. Without both states (RD-TS and RD-Int) you cannot define the rate of the reaction, and therefore the RDStep concept fails. What makes much more sense is to define a rate-determining zone (from the RD-Int to the RD-TS), an almost forgotten concept by Yagisawa (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1136877/, see also https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527678211.ch9#), which helps understand which reactants and products affect the kinetics of the reaction.

Best,
Sebastian

On 26/05/2018 23:30, Robert Molt r.molt.chemical.physics|a|gmail.com wrote:

In short, "rate-determining step" is a shorthand way of saying that which is more explicitly and carefully defined in a "rate-determining state." The former is intuitive and clear in its meaning, thinking in terms of a two-state system; the latter considers the problem from the perspective of ensembles of states which lead to a given TS. They are not different except when a two-state model is not applicable to describe the kinetics.


On 5/24/18 2:09 AM, Norrby, Per-Ola Per-Ola.Norrby-x-astrazeneca.com wrote:

So the concept of rate determining state has been around for about a decade now, it came out of the same work as the energetic span model, from Sebastian Kozuch and Saison Shaik. It’s valid, I’m not contesting that, but there isn’t really a conflict. The “rate determining step” is also a valid concept, you just have to define a “step” as done in kinetics, and apply the Curtin-Hammett principle. In short, if a “step” is considered to go to a transition state from the lowest preceding point, not the closest minimum, then the models work out the same. A simple trick really, you calculate the barrier associated with each transition state by looking back to the lowest preceding point that you can reach without passing a higher barrier. In catalysis, that lowest preceding point could be the resting state, another very useful concept that has also been considered dead, but which is handy when trying to predict what will be observable.

 

Also note that the lowest preceding point does not have to lie on the productive reaction path, it can easily be a side path, a thermodynamic dump that just slows the overall kinetics.

 

I haven’t found an article that summarizes this view. It underlies how many of us handled potential energy surfaces decades back, but I never saw it stated explicitly, it was just handed down as essential knowledge in computational groups with expertise in kinetics. I did write a summary in a book chapter a while back, can be found here: http://dx.doi.org/10.1002/9783527646586.ch8

 

/Per-Ola

 

Per-Ola Norrby

Principal Scientist, Computational Pharmaceutics

Pharmaceutical Sciences, AstraZeneca-Gothenburg

 

 

 

From: owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net [mailto:owner-chemistry+per-ola.norrby==astrazeneca.com===ccl.net] On Behalf Of Andrew Rosen rosen__u.northwestern.edu
Sent: den 24 maj 2018 05:34
To: Norrby, Per-Ola <Per-Ola.Norrby===astrazeneca.com>
Subject: CCL: RateDetermining State

 

Anyao,

 

I refer you to the following two papers:

1) "Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates" (https://pubs.acs.org/doi/abs/10.1021/ja9000097)

2) "The Rate‐Determining Step is Dead. Long Live the Rate‐Determining State!" (https://onlinelibrary.wiley.com/doi/full/10.1002/cphc.201100137)

 

From a detailed mechanistic point of view, it is often much more insightful to talk about about a rate-determining state (either transition state or intermediate) than a rate-determining step. The first paper describes the widely used definition of a rate-controlling state and how to compute it. The second paper contains a few short examples of how the rate-determining state differs from the rate-determining step.

 

On Wed, May 23, 2018 at 10:19 PM Anyao Jiao 1425623121(_)qq.com <owner-chemistry*ccl.net> wrote:


Sent to CCL by: "Anyao  Jiao" [1425623121^qq.com]
Dear All,
  I have a simple question regarding RateDetermining State. My reviewers
suggest me to use RateDetermining State rather than Rate-Determining Step
owning to its inaccuracy. Is that right? If we use the Canonical variational
transition-state theory method, how do you calculate the reaction rate of the
RateDetermining State ?     
   Sincerely

   Anyao Jiao




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-- 
Dr. Robert Molt Jr.
r.molt.chemical.physics===gmail.com

-- 
═════════════════════════════════════
          Sebastian Kozuch
═════════════════════════════════════
       Department of Chemistry
 Ben-Gurion University of the Negev 
          Beer Sheva, Israel
           kozuch-.-bgu.ac.il
    http://www.bgu.ac.il/~kozuch
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