My sincerely thanks to Prof. Jason , Prof. Dean, and Prof. Gerald,
Your comments are very helpful for me.
I calculated the total charge of the moiety including hidrogen and its side
chain atoms, that is 0.9597. The value is just for the moiety, I did not
calculate for all atom of the ligand. I mean, the moiety is attached to
other groups as well.
Thanks again!
Best regards,
nadaafiva
On Thu, Jan 22, 2015 at 5:19 AM, Dean Cuebas <deancuebas.missouristate.edu>
wrote:
> J
>
> On 1/21/15, 6:26 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> >On Wed, 2015-01-21 at 11:46 +0800, asdda asa wrote:
> >> I am performing the parameterization of a ligand using AM1-BCC. The
> >>ligand
> >> contain nitrogen atom which was doubly bound to one carbon atom, singly
> >> bound to other nitrogen atom, and singly bound to other carbon atom, so
> >>the
> >> nitrogen atom has 4 valence. I noticed that the partial charge of the
> >> nitrogen atom was -0.013400. Is this partial charge common, I supposed
> >> previously that the charge for the nitrogen atom was about +1. I would
> >>be
> >> grateful for any comment.
> >
> >This doesn't seem unusual to me. Nitrogen is slightly more
> >electronegative than carbon (and obviously has the same
> >electronegativity as itself), so I would expect it to *maybe* take more
> >electron density than the carbon.
> >
> >Note another molecule that has nitrogen with a valence of 4 -- Lysine.
> >It is connected to 3 hydrogens and a carbon, and has a charge of -0.3854
> >in the Amber force field. The whole moiety has a net charge of +1, but
> >the nitrogen itself is more electronegative than its neighbors, so it
> >takes on a negative partial charge and the positive charges of the
> >neighboring hydrogens (0.34) combines to yield a net charge of +1.
>
> Just a quick note on the topic. Determining formal charges would predict
> that
> N would be +1. Unfortunately formal charges, although they are good for
> accounting
> for Lewis structures, they do not correctly predict the electrostatic
> potential
> (point charges) associated with structure. The charge delocalization is
> determined
> by electronegativity consideration as Jason has just mentioned, not formal
> charge determination.
> It¹s as easy trap to fall intoŠ
>
> Dean--
> Dr. Dean Cuebas, Associate Prof of Chemistry
> deancuebas.missouristate.edu
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
>
>
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Received on Wed Jan 21 2015 - 16:30:02 PST
