Subject: Pi-stacking in MOPAC

From: [email-masked] (Mirko Kranenburg)
Date: Fri, 21 Jul 1995 13:49:21 +0200

Dear Netters,

Several people asked me to summarize the answers to the question:

>Dear Netters,
>
>Currently I am performing geometry optimizations on compounds in which
>pi-stacking has an important contribution to the overall geometry.
>The results from MOPAC 6 calculations (AM1, PM3 and MNDO) show no pi-
>stacking whatsoever, even when a X-ray structure was used as input.
>
>My question: does MOPAC take pi-stacking into account, and are there any
>relevant references concerning this problem.

In addition I found one other relevant reference:
Kurita, Y.; Takayama, C.; Tanaka, S. J. Comput. Chem. 1994, 15, 1013-1018.

I would like to thank everyone who replied!

Here are the answers:

From: [email-masked]
Subject: Re: CCL:pi-stacking in MOPAC?
In-Reply-To: [email-masked] (Mirko Kranenburg) "CCL:pi-stacking in MOPAC?" (Jul
 13, 12:25pm)
To: [email-masked] (Mirko Kranenburg)
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References: <v01510101ac2ac0eb7a59@[145.18.135.53]>

I know of no references, but I can assure you thet no VdW systems were involved
in the parameterization of MNDO,AM1, and PM3....

Regards,

John

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John M. McKelvey                        email: [email-masked]
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From: [email-masked] (Irene Newhouse)
Subject: Re: CCL:pi-stacking in MOPAC?
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No, MOPAC doesn't handle pi-stacking at all.  The problem is, that in these
interactions, the long-r *tails* of the wave functions are involved, which is
rather different from the situation for which the parameters are derived!
I've done some work in this area, & have a folder of references somewhere- I'd
have to dig them out.  S. Fraga, in Canada, wrote a program that uses a force-
field to compute the intermolecular interactions between molecules of fixed
geometry that I've found works rather well.  This work has been recently ex-
tended by R. E. Cachau.  A. Warshell claims that his program, available for
purchase or as a QCPE version, will do intermolecular interactions, but I've
found it to be rather flaky, to be honest.  If you don't have access to an
on-line catalog that can help you find these refs., let me know & I'll try to
find my file...

Irene Newhouse

From: [email-masked] (Steve Bowlus)
Subject: pi-stacking in MOPAC
To: "[email-masked]"@SNDZEH.dnet.sandoz.com
Cc: [email-masked]
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I would be interested in any useful replies.

I'm also interested in formation of aromatic-aromatic complexes, in which
pi-stacking is one possible form of interaction.  I've not had experimental
results to compare, but the structures I've dealt with seemed reasonable,
given the normal amount of jiggling about to relieve steric interactions (
these are not the simplest of aromatics!)

sb

===========================================================================
  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
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From: [email-masked] (Dr. Daniel L. Severance)
Subject: Re: CCL:pi-stacking in MOPAC?
In-Reply-To: [email-masked] (Mirko Kranenburg) "CCL:pi-stacking in MOPAC?" (Jul
 13, 12:25pm)
To: [email-masked] (Mirko Kranenburg)
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  Hi,
    You need to take into account the other interactions going on in the
crystal
structure.  It's likely that pi-stacking isn't a minimum, but rather, the
residual required to allow the other interactions to take place...
    Dan

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Dr. Daniel L. Severance                 [email-masked]
Staff Researcher                        Work phone:     (415) 354-7509
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From: [email-masked]
Subject: Re: CCL:pi-stacking in MOPAC?
To: [email-masked]
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Dear Mirko:

Interesting question. Could you please send me a summary and or the answers
you get?
Thanks a lot in advance.

Sincerely,

Guillermo A. Morales

internet: [email-masked]

From: Ernest Chamot <[email-masked]>
Subject: Re: CCL:pi-stacking in MOPAC?
To: Mirko Kranenburg <[email-masked]>
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Dear Mirko,

I am not surprised that:

>Currently I am performing geometry optimizations on compounds in which
>pi-stacking has an important contribution to the overall geometry.
>The results from MOPAC 6 calculations (AM1, PM3 and MNDO) show no pi-
>stacking whatsoever, even when a X-ray structure was used as input.
>

At one point I was trying to model charge transfer complexes, which should
have a pi stacking interaction.  I assume this would be similar to the
system you are trying to study.  I had a GREAT deal of difficulty getting
Mopac to find any stable complex, even when I (as you) started with two
molecules in their relative positions as determined by X-ray diffraction.  I
did finally find one ever so slightly stable local minimum.  At least in my
experience (and evidently in yours) the packing forces may be too weak
relative to other contributions to energy for Mopac to optimize effectively.
It may just be that they are in fact weak, but I would have thought them to
be significant for a charge transfer complex.  I suspect that the
wavefunctions in AM1 and PM3 formalisms do not have enough diffuse character
to model the longer range interactions correctly.

This is only my own observation, so if you get replies confirming this as a
weakness, or identifying some other cause of the problem, I would like to
hear them.  Thanks.

EC
---
Ernest Chamot
Consultant in Computational Chemistry Applications
Chamot Labs, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
[email-masked]
Phone/Fax: (708) 637-1559

From: [email-masked]
Subject: Re: CCL:pi-stacking in MOPAC?
To: [email-masked]
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Mirko,
        We,too, have experienced what you state: no evidence of pi stacking
in any of the semi-empirical methods.  We have found an attraction using
either HF or MP2 calculations, however (not yet published).
        Ned Martin
**********************************************************************
Ned H. Martin, Chair
Department of Chemistry
University of North Carolina at Wilmington      Voice: 910-395-3453
601 S. College Rd                               Fax:   910-395-3013
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From: [email-masked] (Dr U. Koch)
Subject: Re: CCL:pi-stacking in MOPAC?
In-Reply-To: <v01510101ac2ac0eb7a59@[145.18.135.53]> from "Mirko Kranenburg" at
 Jul 13, 95 12:25:58 pm
To: [email-masked] (Mirko Kranenburg)
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Dear Mirko,

which system are you looking at?
Generally, 2 contributions are normally important
for the geometry of pi-pi interactions: Dispersion,
which favours maximum overlap between the pi systems
and electrostatics. Since the dispersion energy
is included in the quantumchemical correlation energy,
you can't expect to reproduce it by calculations on
the SCF level. The electrostatic part is often determined
by a signifcant anisotropy of the atomic charge distribution
(pi-densities). To reproduce these you need polarizable
basis functions. I think for pi-pi interactions force field
methods with a more sophisticated description of the electrostatics
(see: S.L. Price , A.J. Stone , JCP 86 (1987), 2859 or C.A. Hunter
and J.K.M. Sanders, JACS 112 (1990), 5525) are often a good alternative.

Best wishes

             Uwe  Koch

From: " (Thomas Bally)" <[email-masked]>
Subject: Re: CCL:pi-stacking in MOPAC?
To: " (Mirko Kranenburg)" <[email-masked]>
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Dear Mirko,

>Currently I am performing geometry optimizations on compounds in which
>pi-stacking has an important contribution to the overall geometry.
>The results from MOPAC 6 calculations (AM1, PM3 and MNDO) show no pi-
>stacking whatsoever, even when a X-ray structure was used as input.
>
>My question: does MOPAC take pi-stacking into account, and are there any
>relevant references concerning this problem.

  I have encountered the same problem in a different context. The reason
  for the absence of pi-stacking is, that in all of Dewar's semiempirical
  methods (MINDO / MNDO / AM1 / PM3) interaction between pi-systems is vastly
  underestimated at all distances and is nearly zero at distances such as
  they prevail typically in pi-stacked systems. Somehow this appears to be
  a well kept secret as I know of no reference where this is treated in any
  systematic way (we intend to publish a paper on this on occasion).

  I brought up the point at a Faraday Discussion in response to a paper
  presented there by Tim Clark (see: J. Chem. Soc. Farad. Trans. 90, p.
  1808 (1994), in particular Fig 6 and the corresponding text on this page).
  In a later contribution on the same topic, Josef Michl mentioned a paper
  by a group from Du Pont (J.Am. Chem. Soc. 98, 8401 (1976)) who have
  apparently attempted to remedy the situation, but with no success.

  I don't know where the problem comes from because the Slater AO's which
  are used to calculate overlaps in all-valence semiempirical methods
  ought to be well suited for that kind of problem. So it is the parametri-
  zation which is to be blamed and this is difficult to fix.  I am in
  correspondence with Mike Zerner, the author of ZINDO, who thinks that he
  knows how one would need to go about doing this properly, but I have not
  heard from him for a while.

  I think if you want to calculate pi-stacked systems you need to go to some
  ab-initio method. DFT is probably also not so good as it often has problems
  with van der Waals type interactions.

  I am sorry that I cannot help you more at this point!

  Best wishes

  thomas

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From: [email-masked] (Kimberley Cousins)
Subject: pi stacking
To: [email-masked]
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I'm hoping this will help.  I do not have the original reference here at
home, and am about to leave the country, so my memory will have to serve.
There is a paper on the 3-D structure of hexaphenylbenzene published about
ten years ago in a less common (Indian?) journal.  Its the only paper that
I know of with calculations of hexaphenylbenzene, and as I recall has some
discussion of pi stacking (or lack there of) in the calculated vs. crystal
structure of this compound.  If you would like more information, and can
wait til after August 1, please email me back and let me know.

Kimberley Cousins
Department of Chemistry
California State University, San Bernardino
5500 University Parkway
San Bernardino, CA  92407

(909)880-5391
[email-masked]

Mirko Kranenburg
Universiteit van Amsterdam
J.H. van 't Hoff Research Institute
Dept. of Inorganic Chemistry and Homogeneous Catalysis
Nieuwe Achtergracht 166
1018 WV Amsterdam
The Netherlands
tel. +31-20-5256417
fax. +31-20-5256456
e-mail: [email-masked]