Subject: Re: CCL:activation barrier

From: [email-masked] (Eberhard von Kitzing)
Date: Wed, 9 Feb 94 13:17:54 +0100

>Hi netters,
>
>I was wondering whether someone can help me with the following problem:
>
>I have done several molecular dynamics simulations of an organic ring
>system at different temperatures using SYBYL. At "low" temperatures only one 
>conformation could be detected (< 2000 K), whereas at high temperatures
>(> 2000 K) an additional conformation occurs. Can I draw any conclusions
>on the height of the activation barrier between the two conformations
>from the dynamics runs?

The inverse of the frequency of flipping should be in the order of the
rate of going from one conformer to the other for a given temperature. 

-------------------------------------------------------------------------

Eberhard von Kitzing
Max-Planck-Institut fuer Medizische Forschung
Jahnstr. 29, D69120 Heidelberg, FRG

FAX : +49-6221-486 459  (work)
Tel.: +49-6221-486 467  (work)
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internet: [email-masked]

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From: [email-masked] (Thomas Slee)
Date: Wed, 9 Feb 1994 10:50:30 -0500

Eberhard von Kitzing writes...
| 
| >I have done several molecular dynamics simulations of an organic ring
| >system at different temperatures using SYBYL. At "low" temperatures only one 
| >conformation could be detected (< 2000 K), whereas at high temperatures
| >(> 2000 K) an additional conformation occurs. Can I draw any conclusions
| >on the height of the activation barrier between the two conformations
| >from the dynamics runs?
| 
| The inverse of the frequency of flipping should be in the order of the
| rate of going from one conformer to the other for a given temperature. 
| 

While this is true for realistic MD simulations, by the time one 
gets to 2000K any current force field is almost completely
INaccurate.  Carrying out high temperature MD runs is still useful as 
a means of conformational searching -- it enables you to shake the 
molecule vigorously to see if it can be jolted into different 
shapes, and generates a set of plausible structures that can be
used for further analysis -- but that vigorous shaking no longer 
has any real relation to the behaviour of the physical system at 
the specified temperature (I'd like to see any organic ring system 
still in one piece at 2000K!).   Any relation between calculated
flipping frequency and actual activation barriers must be at best 
qualitative for these simulations, as you moving over a very 
unrealistic potential barrier.

			Tom Slee
-- 
Tom Slee
Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 
Internet:  [email-masked]		Tel. (519) 725-4040