Subject: SUMMARY: MM calculation of the stacking structures

From: "Michael G. Razumov" <[email-masked]>
Date: Fri, 2 Jun 2000 13:41:23 +0300

Hi!

Some time ago I've asked a question about molecular mechanics calculations
of stacking structures:

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Could anybody help me with a problem, concerning MM calculation of the
stacking structures?

I have (theoretically) two plane aromatic structures (Ni(II)
phtalocyaninates), one above another, bound with each other between benzene
rings by some flexible carbon chains.

The question is: will the planes come off each other if the length of these
chains is long enough? Or will they fix at some distance from each other?

For example, calculating these systems with standard molecular mechanics
with electrostatic interactions turned off, one will result in two planes at
distance about sum of van-der-Waals radii (C-C) as there is a minimum of
this function here.

_Is there any physical sense of such structure?_ Maybe, pi-pi interaction
should be also taken into account?

Probably, I need to turn on electrostatic interactions? If so, were from to
take partial atomic charges?
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Thanks to Luigi Cavallo and Michael Charlton for the help.

/////////////// Luigi Cavallo's <[email-masked]> answer
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To properly simulate benzene dimer, for example, you MUST use atomic
charges. Usually, the C charge is something between -0.10 and -0.15, but
you have to check for the particular force field you're using.

Without charges, the benzene dimer minimizes to a geometry with the 2
rings one on top of the other, at the minimum C-C vdw distance, as you
find. However, this geometry is overstabilized with respect to the "real"
minimum, which has the 2 rings perpendicular each other. At least as it
come from ab initio calculation, as it is in the X-ray structure of solid
benzene, as it comes when you add charges with a MM force field.
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////////////// Charlton, Michael's <[email-masked]> answer
/////////////////////
Although I am no longer involved in modelling PCs, in my old job, my
colleagues examined stacking interactions, and got reasonable lattice /
sumblimation enthalpies using force fields with atom-centred point charges.
We often used AM1 for these charges, but this is not applicable in your Ni
case.  We also used either Gasteiger-Marsili or QEq (from Cerius) charges -
these are more applicable to metals.  I seem to remember relatively little
sensitivity of the lattice energy on the choice of charges.
HOWEVER, Chris Hunter (Sheffield University (UK), and a much greater
authority on these systems than I am) showed that to reproduce pi-pi
stacking geometries effectively, you have to use non atom centred charges.
In particular, he placed partially-charged dummy sites above and below the
system to mimic pi effects and reproduced aromatic stacking very well.  (I
believe he Christened them "Zeds". ) Unfortunately, I don't have a reference
to this work to hand, but you may be able to find Chris on the university
web site.

As a final note, pi-pi stacking makes up a large proportion of the
phthalocyanine packing energy, which is itselfe very strong.  If you are
trying to model pulling the system apart, you will need to include it in
your calculations.
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Michael G. Razumov,  Postgraduate Student of
Kurnakov Institute of General and Inorganic Chemistry
and Lomonosov Moscow State University
E-Mail: [email-masked]  [email-masked]
ICQ UIN: 25169010