Subject: Re: CCL:Question about Electrostatics in Molecular Mechanics

From: [email-masked] (David J. States)
Date: Fri, 4 Aug 1995 10:05:54 -0500

On Aug 3,  4:34pm, BILL WELSH wrote:
> Subject: CCL:Question about Electrostatics in Molecular Mechanics
>
> Dear Netters,
>
> Please help settle a small controversy.  For a particular molecular
> mechanics calculation, I derived partial atomic charges from bond
> dipole moment measurements made in nonpolar solvent.  I then ran
> molecular mechanics calculations using an in vacuo dielectric constant
> of 1.00.  A colleague argues that I must use a dielectric constant
> appropriate to the nonpolar solvent from which the charges were
> derived (e.g., 2-3)....

This is an old controversy.  Most of the dielectric in a nonpolar solvent is
due to electronic polarization that is not modeled by explicit molecular
reorientation in an MD run.  On the otherhand, it may well be incorporated
implicitly into the PE function.  In your example, the issue is how the bond
dipole moment determination was actually done.  Using charges from an
electronic structure calculation or experimental procedure that gave the
intrinsic molecular charge distribution, even if in a solvent cavity, to
calculate a Coulomb term in the a PE function would not implicitly include
solvent screening.  In such case, the electronic polarization dielectric would
need to be explicitly incorporated into the MD calculation.

For the first solvation shell, the continuum dielectric approximation
starts to breakdown.  The solute and a first shell solvent molecule can
be modeled as interacting in vacuo in a cavity surrounded by the continuum
dielectric. There is still significant screening, but it is less than the
continuum dielectric.  So if you really want to do the calculation correctly,
electronic polarization, in addition to molecular reorientation, must
be modeled explicitly.

If the data reduction from an experimental protocol actually resulted
in scaling the charges by the solvent dielectric used in the measurement, then
the MD calculation would actually have to multiply by the dielectric:

	Qi' = Qi/eps
	Qj' = Qj/eps
	Eele = eps*(Qi')*(Qj')/Rij
	     = Qi*Qj/(Rij*eps)

Dipole energy follows same scaling.

David

-- 
David J. States
Institute for Biomedical Computing / Washington University in St. Louis

---

From: [email-masked] (Jeffrey L. Nauss)
Date: Fri, 04 Aug 1995 12:17:03 -0400

>From: [email-masked] (David J. States)
 
>electronic polarization, in addition to molecular reorientation, must
 
The question of calculating electronic polarization explicitly may be
an important one in several situations.  In semi-empirical and ab
initio calculations, I believe polarization is handled explicitly.
(Correct me if I am wrong on this.) However, I am not familiar with
any empirical potential energy function that incorporates polarization
except for that developed in Wilma Olson's group for nucleic acids
(Srinivasan and Olson, J. Biomol. Struc. Dyn. (1987) vol 4, pp
895-938.)  They included in their non-bonded interactions an explicit
charge induced dipole effect between atoms:
 
Dij = 165.9 (delta(i)^2* alpha(j) + delta(j)^2 * alpha(i))
      ----------------------------------------------------
                           epsilon
 
where delta is the partial atomic charge, alpha is the atomic
polarizability, and epsilon is the dielectric constant.  This term
accounts for stacking interactions in nucleic acids.
 
I have never seen a similar term employed in any other forcefield and
have ofter wondered why.  Comments?
 
                                                Jeff Nauss
 
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