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."
Christopher Harrison Ph.D.
Postdoctoral Research Associate
Theoretical and Computational Biophysics Group
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. <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
> 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 <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
> >I think Richard by "transition state" means more an "intermediate".
> >Yahoo! oneSearch: Finally,
> >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
> Boardwalk for $500? In 2007? Ha!
> Play Monopoly Here and Now (it's updated for today's economy) at
> Yahoo! Games.
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