From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Sep 27 2007 - 13:24:13 CDT
I guess we're dealing with two sets of terminologies here, the biochemists' and the physical chemists'.
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: paco ty <typaco_at_inbox.com>
To: Richard Wood <rwoodphd_at_yahoo.com>
Sent: Thursday, September 27, 2007 12:48:30 PM
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation
Of course a transition state is an "intermediate" in common english,
BUT an intermediate (or a series of) according to the terminology of
folding kinetics is at a local minimum between the unfolded minimum
and the minimum of the folded state.
The transition state corresponds allways to the highest FE between
two close local minima.
I think that this is how most collegues interprete these words.
Bye
-----Original Message-----
From: rwoodphd_at_yahoo.com
Sent: Thu, 27 Sep 2007 09:22:57 -0700 (PDT)
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Determining Transition State from an Unfolding Simulation
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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