Re: [AMBER] Chirality of amines in GAFF

From: FyD <>
Date: Wed, 14 Apr 2010 21:51:52 +0200

Dear Dmitry Nilov,

> Amines of the type NHRR' are chiral because of the lone pair of electrons.
> The energy barrier for inversion of stereocenter is about 7 klcal/mol.
> I wonder if there is some mechanism in GAFF to prevent the amine
> inversion. I suppose that 7 klcal/mol barrier crossing is a low-probability
> event on the time scale of MD simulations, nevertheless I've observed
> inversion of my amine during equilibration stage.

I am not sure you are right when you say that a tertiary amine NHRR'
is chiral. I think the nitrogen of such a tertiary amine NHRR' is NOT
asymmetric. I even wonder if this interconversion is not normal: The
only question is how OFTEN during MD simulations this should be
observed. On the contrary, quaternary ammoniums (+)NHRR'R" do have an
asymmetric nitrogen & present an optical activity.

Just my personal opinion...

Please, see (which is ambiguous)
    & better
      & then

regards, Francois

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Received on Wed Apr 14 2010 - 13:00:03 PDT
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