On Monday 17 May 2004 05:47 pm, Bill Ross wrote:
> > I am asking again about the TI of the opening of a ring.
> > I have a 2-Methyl-2,3Dihydro-isoindol-1-one system. I would
> > like to mutate the C3 atom (opposite to the keto group in the
> > 5-membered ring) into an H which is bound to the C-atom next
> > to it in the six-membered ring. The two hydrogens become
> > dummy atoms, and the ca to which they are bound to is mutated
> > into an ha. How do I tell leap now that the ha is not bonded
> > to the nitrogen? When I check the molecule in leap, I need to
> > specify the bond and angle parameters, but since there is no
> > bond, I cannot specify them.
>
> The programmatic reality is that your ha remains bonded to
> the nitrogen. Therefore you need to choose a novel atom
> type for the new hydrogen and assign it parameters that
> are correct on the bonded side and 0 on the disappeared-
> bond side. If the parameters on the two sides overlap,
> you will need to change the type of one of the atoms it
> is bonded to to another novel type and replicate the
> parameters for that type.
>
> Experts may have better advice.
>
> Bill
Well, I wouldn't put myself in the expert category, but I don't
see how you could ever have any confidence in the results of such
a calculation, assuming you can find a way to set the system up
to (apparently) do what you describe. This is an inherently
quantum mechanical "event" you are trying to simulate with a
classical mechanical method. What do others think?
Bud Dodson
--
M. L. Dodson bdodson.scms.utmb.edu
409-772-2178 FAX: 409-772-1790
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Received on Tue May 18 2004 - 00:53:01 PDT
