Re: Determining Transition State from an Unfolding Simulation

From: Eduardo Tejera (
Date: Thu Sep 27 2007 - 15:09:41 CDT

  I think that both opinions are correct. In a first approach the transition state is an extremely unstable structure of maximal energy that is formed between any pair of molecular states (one molecule in two different forms (like descomposition) or two different molecules) in one elementary kinetic step (one of several) and is perflectly possible that the final structure in the elemental kinetic step will be an intermediary structure of the global reacction. One of the characteristic of intermediate species is that it is present in several (minimal two) elemental kinetic steps in order to disappear in the global reaction however this is not applied to the "transition structure".
  The energy diagram showed by Richard correspond to an elementary step however the intermediary concept of Christopher I think that considerer the global reaction (like iodine forms in the BZ reaction).

Christopher Harrison <> escribió:
    Raymond is correct. The classical definition of an intermediate is a short-lived, experimentally observable species that is at a local minimum on the potential energy surface (PES) between transition states. A transition state structure must be a first order saddle point on the PES where the single negative frequency corresponds to the mode of motion describing the collective coordinate change. A transient structure that possesses any negative frequencies is not defined as an "intermediate."



    Christopher Harrison Ph.D.
  Postdoctoral Research Associate
  Theoretical and Computational Biophysics Group
  Beckman Institute
  University of Illinois at Urbana-Champaign
  405 N. Mathews
  Urbana, IL 61801


    On Sep 27, 2007, at 11:22 AM, Richard Wood wrote:

    Then I learned different kinetics.

What about A + B ------------->C?

  | T1
  | _
  | / \
FE|\ / \
  | \_/ \
  | \_
  | A+B C
             Reaction pathway

Now, T1 is an intermediate and a transition state.


  Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959

  ----- Original Message ----
From: Raymond C. Fort Jr. <>
To: Richard Wood <>
Sent: Thursday, September 27, 2007 10:39:26 AM
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation

  At 08:34 AM 9/27/2007, you wrote:
>Isn't an "intermediate" by definition a "transition state"? That's
>how I learned reaction kinetics.

No. An intermediate is a minimum on the potential energy surface; a
transition state is a first order saddle point.

>Richard L. Wood, Ph. D.
>University of Minnesota
>Dept. of Medicinal Chemistry,
>College of Pharmacy
>717 Delaware St. SE
>Minneapolis, MN 55414-2959
>---- Original Message ----
>From: paco ty <>
>Sent: Thursday, September 27, 2007 5:35:14 AM
>Subject: namd-l: Determining Transition State from an Unfolding Simulation
>I think Richard by "transition state" means more an "intermediate".
>Yahoo! oneSearch: Finally,
>search that gives answers, not web links.

Professor Ray Fort Jr.
Department of Chemistry
University of Maine Voice: (207)-581-1180
Orono, ME 04469 FAX: (207)-581-1191

Computer modeling of organic and biomolecules; chemistry of lignin
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