Re: [AMBER] Question of AM1-BCC

From: Dean Cuebas <>
Date: Wed, 21 Jan 2015 15:19:06 -0600


On 1/21/15, 6:26 AM, "Jason Swails" <> 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
>> 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
>> 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
>> 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
N would be +1. Unfortunately formal charges, although they are good for
for Lewis structures, they do not correctly predict the electrostatic
(point charges) associated with structure. The charge delocalization is
by electronegativity consideration as Jason has just mentioned, not formal
charge determination.
Itıs as easy trap to fall intoŠ

Dr. Dean Cuebas, Associate Prof of Chemistry
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

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Received on Wed Jan 21 2015 - 13:30:02 PST
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