Subject: Re: CCL:HyperChem: Incorrect geometries in amines

From: Andy Jennings <[email-masked]>
Date: Tue, 2 Dec 1997 08:40:56 +0000 (GMT)

On Mon, 1 Dec 1997, Paddy Kane wrote:

>  Hi,

Hi Paddy

> 
>  I am a user of HyperChem, version 4. Whenever I use molecular mechanics
> with the MM+ force field, to geometry optimise molecules such as
> Phenylamine (C6H5NH2), the geometry about the N atom is planar rather than
> pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, rather
> than N3 as would be expected. I get the same result with molecules such as
> H2C=CHNH2 or H2C=NNH2. I also get incorrect geometries if I initially use
> the model builder to obtain an approximate geometry for such molecule or
> if I use any of the other three force fields available within HyperChem.
> If I initially set the atom type for the nitrogen atom to be N3, I still
> get an planar geometry about the nitrogen atom. 
> 
>  However, for molecules such as methylamine and cyclohexamine, i.e., where
> the atom bonded to the nitrogen atom is saturated, the correct geometry
> and atom type are obtained for the nitrogen atom. 
> 
>  Has anyone else experienced this problem?

Unless I'm missing the point here what you see is not a problem - simply
the correct answer. The nitrogen in these systems WILL be planar due to
the pi systems delocalising over all conjugated atoms. This forces the
nitrogen into planarity...something which won't happen with a saturated
system as there is no opportunity for pi orbital delocalisation. Might I
suggest reading something like 'A guidebook to mechanism in organic
chemistry' by Peter Sykes which has an excellent chapter on atomic
orbitals and hybridisation.

Cheers,

Andy

> 
>  I would be very grateful if someone could advise me of how to solve the 
> problem. 
> 
>  Kind rgds,
>  Paddy.
> 
=================================================================
Andy Jennings - SmithKline Beecham Pharmaceuticals
Phone: +44 (0) 1279 627682 Fax:  +44 (0) 1279 627685
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"Statistics are like a bikini. What they reveal is suggestive,but
 what they conceal is vital." - Aaron Levenstein
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