From owner-chemistry@ccl.net Sat May 26 18:08:01 2018 From: "Robert Molt r.molt.chemical.physics|a|gmail.com" To: CCL Subject: CCL: RateDetermining State Message-Id: <-53322-180526163053-8632-LT+Jd5m5kGSRrjTm0A0feg,,server.ccl.net> X-Original-From: Robert Molt Content-Language: en-US Content-Type: multipart/alternative; boundary="------------9F014BF805F6A5D7543EFB1C" Date: Sat, 26 May 2018 16:30:43 -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. --------------9F014BF805F6A5D7543EFB1C Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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 > > > > -= This is automatically added to each message by the mailing > script =-
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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
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