Subject: Re: CCL:M:? re partial atomic charges

From: [email-masked] (Per-Ola Norrby)
Date: Mon, 8 Jan 1996 14:28:59 +0100

Dr. Shapiro asked:

>     For some calculations that I wish to perform, I need to have partial
>atomic charges; these I can generate without problems using MOPAC.  However,
>some of the molecules in which I am interested have a lone electron pair
>on an unionised phenolic group, and the software which I am using requires
>that I enter a partial atomic charge for this lone pair.  Since my MOPAC
>(AM1) calculations only generated partial atomic charges for the hydrogen
>and heavy (carbon, oxygen) atoms, is there a single "standard" value for the
>partial atomic charge on this lone pair that I should use, or will the par-
>tial atomic charge on the lone pair vary substantially with the pattern of
>substitution around the phenol ring?  Or should it simply be set equal to
>zero?

        It all hangs on what you are going to use the charges for.  I
assume it's a molecular mechanics/dynamics calculation; in that case, the
charges to use are very much dependent on which force field you want to
use.  Not all force fields will work well with semi-empirically determined
charges, and indeed, "charges from MOPAC" is a very fuzzy term.  Are you
talking about some kind of ESP charges, or are you using (shudder :-) raw
Mulliken charges, or what?

        I only know about lone pairs in the MM2 paradigm.  There, they are
included mainly to reproduce an anisotropic van der Waals surface, and
should not participate in electrostatics at all.  Of course, MM2 does not
use partial charges for it's electrostatics, so the paradigm might be
different...  Doesn't the program come with a recommendation for situations
like this?  If not, I'd start by guessing no partial charge on the lone
pairs.

        Per-Ola Norrby

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---

From: [email-masked] (Peter Shenkin)
Date: Mon, 8 Jan 96 10:50:14 -0500

> Date: Mon, 8 Jan 1996 14:28:59 +0100
> From: [email-masked] (Per-Ola Norrby)

> >some of the molecules in which I am interested have a lone electron pair...
 ...
> ... the

All true, but independent of the lone-pair problem.

>         I only know about lone pairs in the MM2 paradigm. ...

By the way, Amber, until Amber94, used lone pairs on S.

>...There [[ i.e., in MM2 ]], they are
> different...  

MM2 electrostatics, by default, uses bond moments interacting as dipoles,
and bonds to lone pairs do have moments in MM2.  So the lone pairs
do indeed contribute to electrostatics in MM2.

What I'd do is take whatever bond moments your force-field uses
for the X-Lp bonds and apply them to your semi-empirical charge
distribution.  This will distribute charge between each X and its 
Lp's, keeping the net charge on each X and its associated Lp's equal 
to the original semi-empirical charge on X.  This assumes that your 
semi-empirical charge distribution makes sense in the first place.

(If you've obtained torsional profiles using semi-empirical methods,
you'd probably then want to go back and "trim" the torsional parameters
so that the overall shape of the molecular mechanics torsional
profile is matched by the force-field when all terms, including
electrostatic and vdW, are used.)

	-P.
* It's not the road, not the journey, it's the shock absorbers. (H.T.Deane)*
*** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., ***
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