Subject: Peptide rotation barriers

From: Michael Nolan <[email-masked]>
Date: Thu, 29 Oct 1998 12:46:09 +0000 (GMT)

Dear all,

I'm studying the link formed between p-aminophenol (AP) and p-hydroxybenzoic acid (HBA). The bond formed between
the two molecules is the peptide link 

		X	    O
		 \	   /
	          \	  /
		   N-----C
		  /	  \
		 /	   \
	        H	    X

Now according to the biochemists the most stable conformation is the trans configuration (steric reasons etc etc)
We computed a rotational barrier (trans->cis for HBA-AP), simply by stepping 15 degree incremenets along the
torsion X-N-C-O and calculating single point energies(our resources are so meagre that we cannot do optimisations
for each structure). We used B-LYP/6-31G* and also the PCFF force-field. B-LYP gave a large barrier (hundreds of
kCal/mol) and the FF gave ridiculous results. At least we could see that the barrier to rotation from trans to cis
is very high, which I guess you would expect. 

I have a couple of questions....

1: Would it be in people's opinion valid to use PCFF for MD simulations of this system? Bearing in mind for HBA
we used the PCFF force-field successfully and I guess we would like to be consistent in our use of force-field.

2: Is it valid to estimate the barrier to rotation around the peptide link only from single point calculations?

3: Has anyone looked at this barrier before? I have looked at a number of databases for AP and only got rubbish
and a chemical abstracts search was none too successful. I would appreciate any refs. at all 

Summary as usual

Thanking you for your time

Michael

**************************************************************************
Mr. Michael Nolan	
Materials Modelling Section, Advanced Materials and Technologies Group
National Microelectronics Research Centre  	
Lee Maltings, Prospect Row				   	
Cork
IRELAND

mail: [email-masked]

Tel:   + 353 21 90 4113

http://nmrc.ucc.ie/projects/ape/
http://nmrc.ucc.ie/groups/AMT/modellingRes.html

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