From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Sep 27 2007 - 14:28:49 CDT
The sentence, "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." is incorrect. An intermediate is a species in a reaction that can be isolated and put in a bottle, as my undergraduate advisor used to tell us. A "transition state" is a species that generally cannot be isolated, such as in the following reaction:
H2S2 + HS- ----> H2S- + H2S
In this reaction, you get a "transition state", which is non-isolable, because there is a bond partially broken and partially formed, and is H3S3-. This is a reaction I have followed computationally using Gaussian to find the structure of the transition state.
If anyone would like to see a picture of this, I can ssend it to them.
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN
55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Christopher Harrison <char_at_ks.uiuc.edu>
To: Richard Wood <rwoodphd_at_yahoo.com>
Cc: namd-l_at_ks.uiuc.edu
Sent: Thursday, September 27, 2007 11:45:16 AM
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation
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."
Chris
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
char_at_ks.uiuc.edu
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
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Raymond C. Fort Jr. <rcfort_at_maine.edu>
To: Richard Wood <rwoodphd_at_yahoo.com>
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.
>
>Richard
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
>rwoodphd_at_yahoo.com
>
>---- Original Message ----
>From: paco ty <typaco_at_inbox.com>
>To: namd-l_at_ks.uiuc.edu
>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,
><http://us.rd.yahoo.com/evt=48252/*http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC>mobile
>search that gives answers, not web links.
Professor Ray Fort Jr. rcfort_at_maine.edu
Department of Chemistry chemistry.umeche.maine.edu/fort.html
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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