Re: Determining Transition State from an Unfolding Simulation

From: Christopher Harrison (char_at_ks.uiuc.edu)
Date: Thu Sep 27 2007 - 11:45:16 CDT

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
> and cellulose
>
>
>
>
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> Play Monopoly Here and Now (it's updated for today's economy) at
> Yahoo! Games.

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