From owner-chemistry@ccl.net Fri Jul 21 07:58:00 1995 Received: from vax3.sara.nl for mirko@SARA.NL by www.ccl.net (8.6.10/930601.1506) id HAA22942; Fri, 21 Jul 1995 07:50:27 -0400 Received: from horus.sara.nl by SARA.NL (PMDF V4.2-15 #2498) id <01HT4UGNQNM8AM3KNO@SARA.NL>; Fri, 21 Jul 1995 13:53:52 +0200 (MET-DST) Received: from hk-pc1.chem.uva.nl by horus.sara.nl (AIX 3.2/UCB 5.64/4.03) id AA46922; Fri, 21 Jul 1995 13:49:21 +0200 Date: Fri, 21 Jul 1995 13:49:21 +0200 From: mirko@SARA.NL (Mirko Kranenburg) Subject: Pi-stacking in MOPAC To: chemistry@ccl.net Message-id: X-Envelope-to: chemistry@ccl.net MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT X-Sender: a412knsm@horus.sara.nl 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@xd88.kodak.com Subject: Re: CCL:pi-stacking in MOPAC? In-Reply-To: mirko@sara.nl (Mirko Kranenburg) "CCL:pi-stacking in MOPAC?" (Jul 13, 12:25pm) To: mirko@SARA.NL (Mirko Kranenburg) Message-Id: <9507130903.ZM14423@xd88.kodak.com> X-Envelope-To: a412knsm@horus.sara.nl Mime-Version: 1.0 X-Mailer: Z-Mail (3.0.0 15dec93) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7BIT References: 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@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From: newhoir@duc.auburn.edu (Irene Newhouse) Subject: Re: CCL:pi-stacking in MOPAC? To: mirko@SARA.NL Message-Id: <9507131308.AA26317@mallard.duc.auburn.edu> X-Envelope-To: a412knsm@horus.sara.nl Content-Transfer-Encoding: 7BIT 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@palres.dnet.sandoz.com (Steve Bowlus) Subject: pi-stacking in MOPAC To: "mirko@SARA.NL"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com Message-Id: <199507131453.AA10374@tigger.jvnc.net> X-Envelope-To: a412knsm@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@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From: dan@sage.syntex.com (Dr. Daniel L. Severance) Subject: Re: CCL:pi-stacking in MOPAC? In-Reply-To: mirko@SARA.NL (Mirko Kranenburg) "CCL:pi-stacking in MOPAC?" (Jul 13, 12:25pm) To: mirko@SARA.NL (Mirko Kranenburg) Message-Id: <9507130845.ZM3630@sage.syntex.com> X-Envelope-To: a412knsm@horus.sara.nl Mime-Version: 1.0 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7BIT References: 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@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@LSUVAX.SNCC.LSU.EDU Subject: Re: CCL:pi-stacking in MOPAC? To: mirko@SARA.NL Message-Id: <01HSTKAHYE1EA2HA17@LSUVAX.SNCC.LSU.EDU> X-Envelope-To: a412knsm@horus.sara.nl X-Vms-To: IN%"mirko@SARA.NL" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT 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@sn01.sncc.lsu.edu From: Ernest Chamot Subject: Re: CCL:pi-stacking in MOPAC? To: Mirko Kranenburg Message-Id: X-Envelope-To: a412knsm@horus.sara.nl X-Mailer: VersaTerm Link v1.1.6 Content-Transfer-Encoding: 7BIT 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@xnet.com Phone/Fax: (708) 637-1559 From: MARTINN@UNCWIL.EDU Subject: Re: CCL:pi-stacking in MOPAC? To: mirko@SARA.NL Message-Id: <01HSTNBZQ3WI8WVZNH@UNCWIL.EDU> X-Envelope-To: a412knsm@horus.sara.nl X-Vms-To: IN%"mirko@SARA.NL" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT 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@vxc.uncwil.edu ********************************************************************** From: uk10000@cus.cam.ac.uk (Dr U. Koch) Subject: Re: CCL:pi-stacking in MOPAC? In-Reply-To: from "Mirko Kranenburg" at Jul 13, 95 12:25:58 pm To: mirko@SARA.NL (Mirko Kranenburg) Message-Id: X-Envelope-To: a412knsm@horus.sara.nl X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Transfer-Encoding: 7BIT Content-Length: 833 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)" Subject: Re: CCL:pi-stacking in MOPAC? To: " (Mirko Kranenburg)" Message-Id: X-Envelope-To: a412knsm@horus.sara.nl Content-Identifier: Re: CCL:pi-st... Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT X400-Content-Type: P2-1984 (2) X400-Mts-Identifier: [/PRMD=switch/ADMD=arcom/C=CH/;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 *-------------------------------------------------------------------------* | Prof. Thomas Bally | E-mail: Thomas.Bally@unifr.ch | | Institute for Physical Chemistry | WWW page: | | University of Fribourg | http://sgich1.unifr.ch/pc.html | | Perolles | | | CH-1700 FRIBOURG | Tel: 011-41-37 29 8705 | | Switzerland | FAX: 011-41-37 29 9737 | *-------------------------------------------------------------------------* From: kcousins@wiley.csusb.edu (Kimberley Cousins) Subject: pi stacking To: mirko@SARA.NL Message-Id: <199507180538.AA07605@wiley.csusb.edu> X-Envelope-To: a412knsm@horus.sara.nl X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Transfer-Encoding: 7BIT Content-Length: 764 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@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@sara.nl