Re: Determining Transition State from an Unfolding Simulation

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 and cellulose Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. Free 3D Marine Aquarium Screensaver - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium ____________________________________________________________________________________ Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting

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