From owner-chemistry@ccl.net Mon May 28 05:15:00 2018 From: "Mikhail F. Budyka budyka ~~ icp.ac.ru" To: CCL Subject: CCL: RateDetermining State Message-Id: <-53325-180528050235-8848-Sn8pi/0nunbLS8NzEJnLuQ]|[server.ccl.net> X-Original-From: "Mikhail F. Budyka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 28 May 2018 12:05:09 +0300 MIME-Version: 1.0 Sent to CCL by: "Mikhail F. Budyka" [budyka^^^icp.ac.ru] Robert Molt r.molt.chemical.physics]*[gmail.com wrote: > > 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. Some definitions: Rate is a distance between two points divided by time. State is a point in n-dimensional space. Since one point cannot define the rate, we should know two points. And we should know these points only in order to define the distance between them, and then define the rate. Is it very misleading? Mikhail From owner-chemistry@ccl.net Mon May 28 08:07:00 2018 From: "Stefan Guessregen stefan.guessregen**sanofi.com" To: CCL Subject: CCL: NEW DEADLINE, GCC 2018, 14th German Conference on Chemoinformatics Message-Id: <-53326-180528080454-17866-/zmOHwQPTyeaRAKpxtYi7A^server.ccl.net> X-Original-From: "Stefan Guessregen" Date: Mon, 28 May 2018 08:04:53 -0400 Sent to CCL by: "Stefan Guessregen" [stefan.guessregen=sanofi.com] *** Please note that the deadline for submission of contributed talks and research telegrams has been extended to June 22, 2018 *** Dear colleagues and friends, the division Computers in Chemistry (CIC) of the German Chemical Society (GDCh) cordially invites you to participate in the 14th German Conference on Chemoinformatics. The conference will take place November 11-13, 2018 in Mainz, Germany. The conference reflects and highlights the important role of chemoinformatics, which connects the modern information and data-driven world with computational modelling of molecular systems. It spans a wide range of subjects related to the use of computers in chemistry, pharmacy, materials science and biology; from informatics and data science to atomistic modelling, and from fundamental academic research to industrial applications. Confirmed Speakers: * Yulia Borodina, FDA, USA * Nathan Brown, BenevolentAI, GB * Zoe Cournia, Academy of Athens, Greece * Gabriele Cruciani, University of Perugia, Italy * Michael Gilson, University of California, San Diego, USA * Stefan Grimme, University of Bonn, Germany * Johanna Jansen, Novartis, USA * Georgia McGaughey, Vertex Pharmaceuticals, USA * Brian Shoichet, University of California, San Francisco, USA There will be sessions on: * Big Data and Deep Learning * Chemical Information * Chemoinformatics and Drug Discovery * Databases and Data Handling * Materials Sciences * Molecular Modelling and Design * Protein Modelling * Simulations * Structure Determination * Target and ADMETox prediction The scientific programme will include plenary and contributed lectures, posters and software presentations. The language of the conference is English. The extended deadline for submissions of oral contributions and research telegrams is June 22, 2018. The deadline for poster submissions is August 31, 2018. See more details at https://www.gdch.de/gcc2018 Registration will open in May 2018 at: https://www.gdch.de/gcc2018 Hope to see you in Mainz, The organizers From owner-chemistry@ccl.net Mon May 28 10:40:01 2018 From: "Sebastian Kozuch seb.kozuch(-)gmail.com" To: CCL Subject: CCL: RateDetermining State Message-Id: <-53327-180528074359-16682-SuutErYi8HhnkbA25ne/sQ]-[server.ccl.net> X-Original-From: Sebastian Kozuch Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=utf-8 Date: Mon, 28 May 2018 14:43:48 +0300 MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [seb.kozuch!A!gmail.com] On 5/27/2018 11:30 PM, Robert Molt r.molt.chemical.physics]*[gmail.com wrote:

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.



Dear Robert,
I appreciate humor in science, and even sarcasm. But to set the record straight:

The problems with the "rate-determining step" (or rate-limiting, or rate-controlling) were already pointed out by Laidler (1988), Murdoch (1981), Boudart (2003), Ray(1983), Siegbahn(2005), Boyd(1978), to name just a few.
Sadly, I could not find who had the original idea of a "rate determining step", but if someone knows, I would like to see the original article.

Meanwhile, for all these terms that are extremely connected with the "rate-determining state", I found the references:
The idea of the "degree of rate control" was of Charles Campbell (1994)
The addition of the "thermodynamic degree of rate control" came from Stegelman and Campbell (2009)
The "control factor" equation is from Laidler (1988)
The "most abundant reaction intermediate" term is from Boudart (?)  (1984)
The concept of rate-determining zone came from Yagisawa (1995)
The "energy span" idea was coined by Amatore and Jutand (1999)
The "Curtin-Hammett principle" was designed by, surprise, Curtin and Hammett (1954)
The "quasi-stationary" approximation came from Chapman and Bodenstein (1913)
The term "catalysis" is from Berzelius (1836)
The theory of "sarcasm" was invented by Monty Python (1979)

I apologize if I forgot someone, or if I mixed dates and/or people.

Best,
Sebastian

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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