Subject: intermolecular complexes summary

From: <[email-masked]>
Date: Wed, 5 Jun 1996 13:38:33 +0100

Recently I posted a question on modelling intermolecular complexes. I enclose a
summary. Thanks to all who replied.
Paul Heelis

Original Question

Dear Ccl people,
>Has anyone tried to model intermolecular complex formation. I am interested in
nitrogen heterocyclics, which appear to form a spectroscopically distinct
complex when both oxidised and reduced form are present in equal amounts. Is a
valid approach to ask a semi-empirical programm to optimise a file containing
both molecules in close proximity? and how close to start from?

Any answers will be summarised for the group.

REPLIES

1. We routinely model various complexes in MOPAC (and its brethren).  We usually
will start with a trial geometry from a molecular mechanics
calculation.  Our major problem is that there may be several structures which
are consistent with whatever experimental evidence you have to compare. Getting
a unique answer to a question may thus be impossible, but it is instructive to
see which types of interactions may be operative.

===================================================  Stephen B. Bowlus, Ph.D.
Computer-Aided Molecular Design
                                          Research Division
  e-mail: [email-masked]               Sandoz Agro, Inc.
  Phone:  + 1 415 354 3904                975 California Ave.
  Fax:    + 1 415 857 1125                Palo Alto, CA 94304          

2. Regarding your question, a few comments:

(1) Depending on the nature of your bonding, you could select a value
    between normal covalent bond length and vdw distance. Try to run
    a constrained optimization first with constraints of such bond(s)
    which allow the rest of degrees of freedom settled, and then release
    the constraint and carry out a full geometry optimization.

(2) Alternative is to do a coordinate driving, driving a distance from
    covalent distance to vdw distance with N step. Watch the energy
    of these N sub structure and see there is any minimum there.

(3) SE methods are not parameterized for weakly bonded complex with
    small interaction energy (bond energy). High level theories might
    have to used to calibrate such. Try a model system for a control
    test.

Hope these help!

--Wayne

--
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|  Wayne Huang, Ph.D.           |  18401 Von Karman, Suite 370  |
|  Computational Chemist        |  Irvine, California 92715     |
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3.
I presume that you have some kind of charge-transfer complex. Calculations on
complexes should be possible just like with regular molecules, as the "complex"
is a molecule, just with some bonds weaker than normal covalent bonds. Your
systems are reminiscent of hydroquinone/quinone (quinhydrone) complexes--look
these up in the lit. If you have a GUI with spacefilling models, dock the two
species till they are in contact (van der Waals separation, then merge the files
and optimize (if you can use Spartan you are lucky). Yes, it should be OK to
treat the "supermolecule" as a single file.  For deltaE, watch out for
BSSE---well-known in ab initio,
but I'm not sure how one treats it in semiemp.
Good Luck
Errol Lewars