From:	states(-(at)-)rucola.WUStL.EDU (David J. States)
Date:	Fri, 4 Aug 1995 10:05:54 -0500
Subject:	Re: CCL:Question about Electrostatics in Molecular Mechanics

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


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