molecular modelling of guanidinium/carboylate interaction
Dear Netters!
A biochemist, who uses Insight/Discover and Macromodel came along
with an interesting question concerning molecular modelling. I pass
it on to the net, hoping to find experts in this field. Here is
the problem:
The interaction of a guanidinium function and a carboxylate fnc
was modelled using the software cited above (I do not know, which
force fields they used).
N---H - - - O
/ \
/ \
R---N---C + - C---R
\ /
\ /
N---H - - - O
In either case they did not obtain a planar geometry. Indeed, the
COO turns out to be almost perpendicular to the C(NH)2 plane, which
is not, what one would intuitively assume to be realistic. So what
might have gone wrong? They don't have any idea, and I (as a new-
comer to the field of MM) only have some vague assumptions. If
you have any experience with such systems, please contact me!
Thank you!
L. Ackermann
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* Dr. Lutz Ackermann *
* *
* Lehrstuhl fuer Theoretische Chemie (TU Munich) *
* Lichtenbergstr. 4 *
* 85747 Garching *
* Germany *
* *
* room Nr. 63103 *
* Tel. (+49 +89) 3209 3602 *
* Fax (+49 +89) 3209 3622 *
* e-mail ackerman()at()theo1.theochem.tu-muenchen.de
*
* *
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