Pi-stacking in MOPAC



 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: lrbu00 - at - xd88.kodak.com
 Subject: Re: CCL:pi-stacking in MOPAC?
 In-Reply-To: mirko - at - sara.nl (Mirko Kranenburg) "CCL:pi-stacking in
 MOPAC?" (Jul
  13, 12:25pm)
 To: mirko - at - SARA.NL (Mirko Kranenburg)
 Message-Id: <9507130903.ZM14423 - at - xd88.kodak.com>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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 References: <v01510101ac2ac0eb7a59 - at - [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
 --
 John M. McKelvey                        email: mckelvey - at - Kodak.COM
 Computational Science Laboratory        phone: (716) 477-3335
 2nd Floor, Bldg 83, RL
 Eastman Kodak Company
 Rochester, NY 14650-2216
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 From: newhoir - at - duc.auburn.edu (Irene Newhouse)
 Subject: Re: CCL:pi-stacking in MOPAC?
 To: mirko - at - SARA.NL
 Message-Id: <9507131308.AA26317 - at - mallard.duc.auburn.edu>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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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: bowlus - at - palres.dnet.sandoz.com (Steve Bowlus)
 Subject: pi-stacking in MOPAC
 To: "mirko - at - SARA.NL" - at - SNDZEH.dnet.sandoz.com
 Cc: BOWLUS - at - sandoz.com
 Message-Id: <199507131453.AA10374 - at - tigger.jvnc.net>
 X-Envelope-To: a412knsm - at - horus.sara.nl
 Content-Transfer-Encoding: 7BIT
 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: bowlus - at - sandoz.com               Sandoz Agro, Inc.
   Phone:  + 1 415 354 3904                975 California Ave.
   Fax:    + 1 415 857 1125                Palo Alto, CA 94304
 ===========================================================================
 From: dan - at - sage.syntex.com (Dr. Daniel L. Severance)
 Subject: Re: CCL:pi-stacking in MOPAC?
 In-Reply-To: mirko - at - SARA.NL (Mirko Kranenburg) "CCL:pi-stacking in
 MOPAC?" (Jul
  13, 12:25pm)
 To: mirko - at - SARA.NL (Mirko Kranenburg)
 Message-Id: <9507130845.ZM3630 - at - sage.syntex.com>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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 References: <v01510101ac2ac0eb7a59 - at - [145.18.135.53]>
   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
 --
 Dr. Daniel L. Severance                 dan - at - sage.syntex.com
 Staff Researcher                        Work phone:     (415) 354-7509
 Syntex Discovery Research               Home phone:     (415) 969-5818
 R6W-002                                 Fax (Work):     (415) 354-7363
 3401 Hillview Ave
 Palo Alto, CA  94303
 From: CHMORA - at - LSUVAX.SNCC.LSU.EDU
 Subject: Re: CCL:pi-stacking in MOPAC?
 To: mirko - at - SARA.NL
 Message-Id: <01HSTKAHYE1EA2HA17 - at - LSUVAX.SNCC.LSU.EDU>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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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: chmora - at - sn01.sncc.lsu.edu
 From: Ernest Chamot <echamot - at - xnet.com>
 Subject: Re: CCL:pi-stacking in MOPAC?
 To: Mirko Kranenburg <mirko - at - SARA.NL>
 Message-Id: <echamot.1156040293A - at - quake.xnet.com>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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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
 echamot - at - xnet.com
 Phone/Fax: (708) 637-1559
 From: MARTINN - at - UNCWIL.EDU
 Subject: Re: CCL:pi-stacking in MOPAC?
 To: mirko - at - SARA.NL
 Message-Id: <01HSTNBZQ3WI8WVZNH - at - UNCWIL.EDU>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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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
 Wilmington, NC 28403-3297                       martinn - at - vxc.uncwil.edu
 **********************************************************************
 From: uk10000 - at - cus.cam.ac.uk (Dr U. Koch)
 Subject: Re: CCL:pi-stacking in MOPAC?
 In-Reply-To: <v01510101ac2ac0eb7a59 - at - [145.18.135.53]> from
 "Mirko Kranenburg" at
  Jul 13, 95 12:25:58 pm
 To: mirko - at - SARA.NL (Mirko Kranenburg)
 Message-Id: <m0sWVMy-0007adC - at - grus.cus.cam.ac.uk>
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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)" <Thomas.Bally - at - unifr.ch>
 Subject: Re: CCL:pi-stacking in MOPAC?
 To: " (Mirko Kranenburg)" <mirko - at - SARA.NL>
 Message-Id: <v02110100ac2d9c2951dc - at - [134.21.16.221]>
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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: kcousins - at - wiley.csusb.edu (Kimberley Cousins)
 Subject: pi stacking
 To: mirko - at - SARA.NL
 Message-Id: <199507180538.AA07605 - at - wiley.csusb.edu>
 X-Envelope-To: a412knsm - at - horus.sara.nl
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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
 kcousins - at - wiley.csusb.edu
 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: mirko - at - sara.nl