From inoue@greencross.co.jp Tue Apr 12 02:12:03 1994 Received: from uucp0.iij.ad.jp for inoue@greencross.co.jp by www.ccl.net (8.6.4/930601.1506) id BAA02674; Tue, 12 Apr 1994 01:56:32 -0400 Received: from wincgw1.winc.ad.jp (wincgw1.winc.ad.jp [202.15.200.1]) by uucp0.iij.ad.jp (8.6.8+2.4Wb/3.3Wb-UUCP) with SMTP id OAA11370 for ; Tue, 12 Apr 1994 14:56:29 +0900 Received: by wincgw1.winc.ad.jp (5.67+1.6W/4.18:3.7:winc:931216) id AA25773; Tue, 12 Apr 94 14:56:48 JST Received: by gccss2.greencross.co.jp (4.1/6.4J.6-agu4) id AA20880; Tue, 12 Apr 94 14:10:36 JST Date: Tue, 12 Apr 94 14:10:36 JST From: inoue@greencross.co.jp (Y. Inoue) Message-Id: <9404120510.AA20880@gccss2.greencross.co.jp> To: chemistry@ccl.net Subject: AutoNom - structure to name conversion Dr.Douglas A. Smith noted: >AutoNom was at that time limited to certain functional groups and no 3D >stereochemistry. I don't know what the folks at the Beilstein Institute, >who are developing the software, have done since. I know better programs. One is Japanese JICST JOIS online-service, Chemical Dictionary Database. It can convert names to 3D-structure, or structures to names. I have heard it contains more than 400,000 sub- structures and correct-conversion rate is more than 99%. Please ask JICST. tel:+81-3-3581-6411 fax:+81-3-3593-3375 And the other one is programmed by Dr.Ikutoshi Matsuura. Because I do not know well, please ask him. Maybe it runs on Vax. Clinical Analysis Div., Chugai Pharm., 2-14-1 Kyobashi, Chuo-ku, Tokyo 104 JAPAN. fax:+81-3-3567-6785. Hope this help and interest. Yoshihisa INOUE the Green Cross Corp. inoue@greencross.co.jp From F66269@VM.BIU.AC.IL Tue Apr 12 05:12:06 1994 Received: from phem3 for F66269@VM.BIU.AC.IL by www.ccl.net (8.6.4/930601.1506) id EAA03488; Tue, 12 Apr 1994 04:19:05 -0400 Received: from VM.BIU.AC.IL (MAILER@BARILVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01HB2OVANV9S99G7U9@phem3.acs.ohio-state.edu>; Tue, 12 Apr 1994 04:18:58 EDT Received: from BARILVM (NJE origin F66269@BARILVM) by VM.BIU.AC.IL (LMail V1.2a/1.8a) with BSMTP id 9723; Tue, 12 Apr 1994 11:18:33 +0300 Date: Tue, 12 Apr 94 11:02:57 IDT From: ariel Subject: ab-initio calc with argon To: chemistry@ccl.net Message-id: <01HB2OVANV9U99G7U9@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT To anyone who knows! I do ab-initio calculation on cyano-bicyclobutane and now I want to calculate its energy when Argon is fixed in a distance from C-3 in 6-31+G* basis-set. Argon is not included in it so I want to use the CEP basis set for it only and 6-31+G* for the cyano-bcb molecule. I would appreciate if someone will write to me exactly how to do it in the input file. comment: I use z-matrix in the input file. thanks, ariel From thys@schs.uia.ac.be Tue Apr 12 10:12:13 1994 Received: from sch2.uia.ac.be for thys@schs.uia.ac.be by www.ccl.net (8.6.4/930601.1506) id JAA06640; Tue, 12 Apr 1994 09:19:30 -0400 Received: from localhost by sch2.uia.ac.be (8.6.4/Ultrix3.0-C) id PAA17178; Tue, 12 Apr 1994 15:18:04 +0200 Date: Tue, 12 Apr 1994 15:18:00 +0200 (MET DST) From: Gerd Thys Subject: Summary: IP and EA in semi-empirical methods To: CCL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, A couple of weeks ago, I mailed the following letter to the Computational Chemistry List: I'm looking for articles comparing ionisation-potentials and electron-affinities, obtained by using MINDO/3, MNDO, AM1 and PM3 and experimental data (or ab-initio calculations). I'm especially interested in molecules containing phenyl-, furane-, pyrrole- and thiophene-groups. I already have the articles of M.J.S. Dewar and M.L. Mckee (J.Comp.Chem., p.84 (1983)) and M.J.S. Dewar and W. Thiel (J.Am.Chem.Soc. p.4907 (1977)) on the MNDO results for H,C,N,O and S-containing molecules. I wonder if there are similar articles for the other three methods. Greetings, Gerd The following is a summary of all the replies. I want to thank all these people for their contributions. Another interesting reference, not mentioned in the replies: J.J.P. Stewart, J.Comp.Chem, 10 (1989) 221 (with a comparison of experimental and calculated (PM3, AM1 and MNDO) ionization potentials of 256 compounds) regards, Gerd thys@uia.ac.be ============================================================================== From: Date: Thu, 31 Mar 94 07:57:10 CST Subject: CCL:IP and EA in semi-empirical methods In 1990 J.J.P.Stewart, the author of MOPAC, prepared an extensive comparison of PM3, AM1 and MNDO. It is published as Vol. 4, No.1, of J. of Computer-aided Mol ecular Design, ESCOM, Mar. 1990 (a special issue). Hope this is a help. Pat Plummer, Univ. of Missouri-Columbia ============================================================================== Date: Thu, 31 Mar 1994 09:03:00 -0500 (EST) From: ROBERT LIPNICK 202-260-1274 Subject: CCL: electron affinities In response to your message on CCL today: The following contains experimental and estimated (SPARC) electron affinities for 240 compounds: SH Hilal, LA Carreira, SW Karickhoff, and CM Melton: Estimation of Electron Affinity Based on Structure Activity Relationships, Quant. Struct.-Act. Relat., 12, 389-396 (1993). Bob -----------------------------EPA------------------------- US Environmental Protection Agency Office of Pollution Prevention and Toxics (Mailstop 7403) 401 M Street, SW, Washington, DC 20460 USA TEL: 202-260-1274; FAX: 202-260-1236 or 202-260-1283 EMAIL: lipnick.robert@epamail.epa.gov Robert L. Lipnick, Ph.D., Senior Chemist (QSAR-Toxicology) -----------------------------EPA-------------------------- ============================================================================== Date: Thu, 31 Mar 1994 17:10:51 +0500 From: "Micheal Bartberger" Dear Gerd: Re: your request for papers on ionization potentials and / or electron affinities... There is what seems to be a rather comprehensive paper on this subject (I just picked up the article but haven't looked at it in depth as of yet) in Theoretica Chimica Acta (1994) 87, 415-430. As for your phenyl, furane, and other groups, I do not think that these are given coverage, but perhaps it will be of use to you nonetheless. Hope this helps. Regards, Michael D. Bartberger Department of Chemistry, Physical Organic Division University of Florida bartberg@qtp.ufl.edu ============================================================================== Date: Thu, 31 Mar 1994 11:24:04 -0600 From: Ernie Chamot Subject: References Comparing Calculated IPs and EAs I have been trying to follow the relative accuracy of various methods (molecular mechanics, semiempirical, ab initio SCF, and density functional) in calculating properties for different classes of compounds, and am particular interested in comparisons with experimental data. Here are a couple compilations (which should be a good source of references) and a couple newer references that I found useful because each gave comparisons of ionization potentials or electron affinities for a series of compounds: "Density Functional Methods in Chemistry", Labanowski & Andzelm Ed., Springer- Verlag (1991). "Reviews in Computational Chemistry," Lipkowitz & Boyd, VCH, 1990. W. Thiel, Theo. Chem. Acta., 81, 391- (1992). J. J. P. Stewart, J. Comp. Chem., 12(3), 320-41, 1991. Ziegler & Gutsev, J. Comp. Chem., 13, 70-75 (1992). J. Baker, et. al., J. Comp. Chem., 7(3), 49-58 (1986). Also, the Ampac 4.0, 4.5, and 5.0 literature from Andy Holder summarizes results from testing he, Dewar, and others have done in developing SAM1. I would be very interested in a summary of other references you find useful, if you don't summarize your responses to the CCL. Thanks. EC ============================================================================== Date: Sat, 9 Apr 1994 16:45:44 +0300 From: dodik@yfaat.ch.huji.ac.il (David Danovich) Subject: Ionzation potentials Hi Gerd, I had read you message about ionization potentials and electron affinities. I had implemented a new method (Outer valence Grren Function technique) for semiempirical calculations. It is now a part of MOPAC-93 package. It works very well for organic molecules and esspecially for heterocyclic molecules. You can see results of OVGF calculations with comparison to standard semi empirical calculations in following my articles: 1) D.Danovich, V.Zakrzewski and E.Domnina, J. Mol.Struct (Theochem), 187 (1989) 297-306 2) D.Danovich, V.Zakrzewski and E.Domnina, J. Mol.Struct (Theochem), 188 (1989) 159-166 3) D.Danovich, V.Turchaninov and V.Zakrzewski,J. Mol.Struct (Theochem), 209 (1990) 77-87 4) D.Danovich and Y.Apeloig, J. Chem. Soc., Perkin Trans 2, 1991, 1865-1873 5)D.Danovich, Y.Apeloig and S. Shaik, J. Chem. Soc., Perkin Trans 2, 1993, 321-330. Feel free to ask me if you have any questions. Best wishes David +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. David Danovich Department of Organic Chemistry The Hebrew University of Jerusalem, Givat-Ram Campus, 91904 Jerusalem, Israel ------------------------------------------------------------------------------- Office phone: (972)-2-586934 Internet Addr: dodik@yfaat.ch.huji.ac.il Home phone: (972)-2-789544 FAX number: (972)-2-585345 +=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From SAUNDERS@CHEM.CHEM.ROCHESTER.EDU Tue Apr 12 11:12:13 1994 Received: from chem.chem.rochester.edu for SAUNDERS@CHEM.CHEM.ROCHESTER.EDU by www.ccl.net (8.6.4/930601.1506) id LAA07745; Tue, 12 Apr 1994 11:05:34 -0400 From: Received: from CHEM.CHEM.ROCHESTER.EDU by CHEM.CHEM.ROCHESTER.EDU (PMDF V4.2-14 #6313) id <01HB32VWV5IO00074P@CHEM.CHEM.ROCHESTER.EDU>; Tue, 12 Apr 1994 11:05:30 EDT Date: Tue, 12 Apr 1994 11:05:30 -0400 (EDT) Subject: ab initio calc with argon To: chemistry@ccl.net Message-id: <01HB32VWVYGI00074P@CHEM.CHEM.ROCHESTER.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT In answer to Ariel's question: When one is using a non-standard basis set, the procedure to use is outlined on pp 79 and 117 of the G92 manual (general basis set). As far as I can tell, if a non-standard basis set is used for one atom, the standard ones used for the others must be specified explicitly. They can be obtained in a form suitable for input by running a job with the gfinput keyword. Hope this helps. Bill Saunders From szilagyi@miat0.vein.hu Tue Apr 12 12:12:37 1994 Received: from sztaki.hu for szilagyi@miat0.vein.hu by www.ccl.net (8.6.4/930601.1506) id LAA08305; Tue, 12 Apr 1994 11:46:31 -0400 From: Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id Mi24049; Tue, 12 Apr 1994 17:43:31 +0200 Received: by miat0.vein.hu with SMTP (5.61++/Vein-1.0) id AA23147; Tue, 12 Apr 94 17:47:47 +0200 Message-Id: <9404121547.AA23147@miat0.vein.hu> To: CHEMISTRY@ccl.net Cc: szilagyi@miat0.vein.hu Subject: W-O bond Date: Tue, 12 Apr 94 17:47:47 +0200 X-Mts: smtp X-Charset: US X-Char-Esc: 0 Dear Netters, I am looking for the contact with researchers who carried out theoretical and/or experimental investigations about the tungsten-oxygen bond. I checked the bibliography and no quantitative data was found. Any responses or comments are wellcome. I will summarize for the net. Yours, Rob ------------------------------------------------------------------------------- Robert C. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 h8588szi@ella.hu Egyetem u. 1 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-326016 HUNGARY L4 ------------------------------------------------------------------------------- From ferenc@rchsg8.chemie.uni-regensburg.de Tue Apr 12 13:12:12 1994 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id MAA11083; Tue, 12 Apr 1994 12:58:04 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA08625 (5.65c/IDA-1.4.4 for ); Tue, 12 Apr 1994 18:57:56 +0200 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@ccl.net) id AA02784; Tue, 12 Apr 94 18:55:55 +0200 Date: Tue, 12 Apr 94 18:55:55 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9404121655.AA02784@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: force fields and forces Dear Netters: I was wondering if anybody out there could give me a reference to a good review or book covering the following topics: 1) Where to find a good (and complete) compilation of empirical force field parameters (AMBER, MMX, etc.) 2) How to derive forces acting on individual atoms from a given empirical force field, consisting of e.g.: bond stretch, angle bending, torsional potential terms etc. If there is a common interest, I will report to the net. Thank you very much in advance. Yours sincerely, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way. -- John Paul Jones, USN 1747-1792 ;-) --------------------------------------------------------------------------- From grfamini@cbdcom.apgea.army.mil Tue Apr 12 14:13:21 1994 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.4/930601.1506) id NAA11865; Tue, 12 Apr 1994 13:50:12 -0400 Date: Tue, 12 Apr 94 13:42:03 EDT From: George R Famini To: chemistry@ccl.net Subject: Symposium Announcement Message-ID: <9404121342.aa21843@cbdcom.apgea.army.mil> CALL FOR PAPERS SYMPOSIUM ON APPLICATIONS AND METHODS FOR CONFORMATIONAL ANALYSIS to be held at the National American Chemical Society Meeting in Anaheim, CA April 2-6 1995 (Sponsored by the Division of Computers in Chemistry) Focusing on: New Methods for Conformational Searching The Effects of Solvent on Conformational Preference Conformational Preference of Macromolecules Conformational Preference of Small Molecules The Effects of Conformation on Binding, Reactivity and Physicochemical Properties For Additional Information, contact George R. Famini Joseph J. Urban U.S. Army Edgewood RDE Center SCBRD-RTC (E3160) Aberdeen Proving, MD 21010 (410)671-2670/3332 fax (410)671-1912 email grfamini@apgea.army.mil jjurban@apgea.army.mil From noy@tci002.uibk.ac.at Tue Apr 12 14:14:44 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id OAA12119; Tue, 12 Apr 1994 14:02:23 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA20721 (5.65c/IDA-1.4.4 for ); Tue, 12 Apr 1994 20:02:03 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA22570; Tue, 12 Apr 1994 20:02:01 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9404121802.AA22570@tci002.uibk.ac.at> Subject: Re: CCL:JACS Gopher? Can't decode the TIFF files! To: pacahil@somnet.sandia.gov (Paul A Cahill) Date: Tue, 12 Apr 1994 20:02:01 +0200 (DFT) Cc: chemistry@ccl.net In-Reply-To: <199404112301.RAA25984@somnet.sandia.gov> from "Paul A Cahill" at Apr 11, 94 05:01:16 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1372 : Has anyone had any luck in downloading and then reading the : files available on the American Chemical Society site? I'm trying : to retrieve supplementary material which is apparently stored as a : "Group 4 Fax" compressed TIFF file. The ftp or gopher transfers work : fine, but I don't have a program that can read the compressed file. : Please respond directly to me. I'll summarize to the net : if there is interest. : Thanks!!! Hallo, I would recommend the program "Xview" written by John Bradley. "Xview" or "xv" can be obtained by anonymous FTP to xview.ucdavis.edu /pub/XView export.lcs.mit.edu /contrib/xview3.2 This program can read many graphics format beside TIFF Group IV Fax. If you use Mosaic, you can also display JACS pictures via WWW ( Mosaic made interface to "xv", I guess ). yours, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- From shenkin@still3.chem.columbia.edu Tue Apr 12 15:12:22 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id PAA13472; Tue, 12 Apr 1994 15:03:31 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA24305; Tue, 12 Apr 94 15:02:16 -0400 From: "Peter Shenkin" Message-Id: <9404121502.ZM24303@still3.chem.columbia.edu> Date: Tue, 12 Apr 1994 15:02:03 -0400 In-Reply-To: Luca Jovine "CCL:Looking for RMS distance calculator" (Apr 11, 12:56pm) References: <9404111056.AA14593@imiucca.csi.unimi.it> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Luca Jovine , CHEMISTRY@ccl.net (Computational Chemistry List) Subject: Re: CCL:Looking for RMS distance calculator Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Apr 11, 12:56pm, Luca Jovine wrote: > Subject: CCL:Looking for RMS distance calculator > > Dear Netters, > > I am looking for a program that could calculate a RMS distance matrix > for a set of homologous molecular structures (possibly in PDB format). > It would be even better if such program allowed to pick which parts of > the structures to compare.... Our program, XCluster, does this as a first step in performing cluster analysis; however, the molecules it takes have to be very highly homologous indeed: they have to be conformers. Extension to a mixed ensemble with a common substructure is something we want to do, but it's not there now. If what you are looking at is homologous proteins, please see Holm and Sander, JMB, 233, p123 (1993). Their similarity measure between two proteins is not the rigid-body RMS, but rather the RMS of corresponding elements of the two internal alpha-carbon distance matrices (or something very close to that). They do have provision for performing frame-shifts and deletions for better aligning the two chains prior to final assignment of the "distance" between the two. XCluster is bundled with the MacroModel modeling package; for more info, try "finger mmod@still3.chem.columbia.edu", or send me email. We have a paper in press with J. Comput. Chem. > "I'll give you a definitive maybe" (Sam Goldwyn) I suppose this is what I said; but at least I didn't say, "In two words: im possible." (also attributed to Sam) :-) -P. -- ********************** "So much for global warming...." ********************* Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ***************************************************************************** From pacahil@somnet.sandia.gov Tue Apr 12 17:12:15 1994 Received: from somnet.sandia.gov for pacahil@somnet.sandia.gov by www.ccl.net (8.6.4/930601.1506) id QAA15707; Tue, 12 Apr 1994 16:54:11 -0400 Received: (from pacahil@localhost) by somnet.sandia.gov (8.6.7/8.6.6) id OAA18366 for CHEMISTRY@ccl.net; Tue, 12 Apr 1994 14:54:38 -0600 Date: Tue, 12 Apr 1994 14:54:38 -0600 From: Paul A Cahill Message-Id: <199404122054.OAA18366@somnet.sandia.gov> To: CHEMISTRY@ccl.net Subject: ACS Gopher and Mac - what works and what doesn't Thanks to everyone who replied to my request about downloading supplementary information from the ACS gopher. With everyone's help I was able to make it work, but there are some obscure problems! As for uncompressing the "Group 4 Fax" scheme, I found that the Graphic Converter 1.78 program mentioned by at least one person and by the ACS instructions WORKS GREAT. BUT, it isn't at the address that the ACS lists. Just use archie to find a site for it archie -m 10 graphicconverter1.78us.cpt.hqx will pull up the first 10 locations. Then I used Stuffit Deluxe to un-binhex it, and again to un-cpt it. This program then will run on a Mac and decompress the ACS tif images. Next: DON'T USE FTP, USE GOPHER to retrieve the images. Every file I retrieved with ftp would not open correctly. But, if I went into gopher, then used SHIFT-D to download via (I used binary, but it probably ? is necessary) kermit, I received files that Graphic Converter could read. Very nice, high resolution. As good as a microform printer, but not as good as careful artwork. As for other machines, I don't have any experience, but several people mentioned xv for unix boxes. The changes in the ftp sites for the programs listed in the ACS information seem to be changing faster than the ACS can keep up with. OVERALL, the idea works very well, thanks for everyone for their help, and I hope this makes life simpler for others... Paul Cahill pacahil@somnet.sandia.gov Sandia National Laboratories Correspondence -- No license required. P.S. standard disclaimer regarding not advertising a particular program applies. From FR035002@YSUB.YSU.EDU Tue Apr 12 18:12:15 1994 Received: from phem3 for FR035002@YSUB.YSU.EDU by www.ccl.net (8.6.4/930601.1506) id RAA16241; Tue, 12 Apr 1994 17:35:35 -0400 Received: from YSUB.YSU.EDU (MAILER@YSUB) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01HB3GITFY4G99F8S0@phem3.acs.ohio-state.edu>; Tue, 12 Apr 1994 17:30:48 EDT Received: from YSUB.YSU.EDU (NJE origin FR035002@YSUB) by YSUB.YSU.EDU (LMail V1.1d/1.7f) with RFC822 id 7470; Tue, 12 Apr 1994 17:24:25 -0400 Date: Tue, 12 Apr 1994 17:23:41 -0400 (EDT) From: Irwin Cohen Subject: basis functions To: chemistry@ccl.net Message-id: <01HB3GJ0ZCKK99F8S0@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Netters: Does anyone know of a reference for (a) projection coefficients for the spherical harmonic (real) d and f functions (g?,h?) from arbitrary cartesian axes a,b,c to x,y,z? and/or (b) two-center overlap formulas (sigma, pi, delta, phi) for these? I refer to the real combinations, (x**2-y**2), for example, although references to the non-standard basis, x**2, for example, would also be welcome. Thanks for listening, Irwin Cohen, FR035002@YSUB.BITNET From AHOLDER@VAX1.UMKC.EDU Tue Apr 12 21:12:16 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id UAA18039; Tue, 12 Apr 1994 20:34:02 -0400 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HB3KTFN1GW9N8CYS@VAX1.UMKC.EDU>; Tue, 12 Apr 1994 19:33:55 CST Date: Tue, 12 Apr 1994 19:33:55 -0600 (CST) Subject: AM1 vs. PM3 To: CHEMISTRY@ccl.net Message-id: <01HB3KTFNUEA9N8CYS@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Netters, A few weeks ago, Jeffrey Nauss asked about a comparison between the AM1 and PM3 semiempirical methods. Both of these semiempirical methods are included in most programs that support semiempirical calculations (AMPAC, MOPAC, etc.). Please note that the following discussion is MY OPINION and a compendium of MY EXPERIENCES. I hope you find it somewhat useful. The lead references to each method follows: AM1: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. PM3: Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209. AM1 stands for "Austin Model 1" and PM3 stands for "Parameterization Method 3". Both methods implement the same basic NDDO theory pioneered by Michael Dewar while at the University of Texas at Austin. The differ- erence is in how the parameters that the semiempirical methods utilize to replace portions of the full ab initio implementation of Hartree-Fock theory. Perhaps the most important difference between AM1 and PM3 is the involvement of the researcher in the parameterization process. PM3 was developed using a largely undirected mathematical optimization process with greatly reduced guidance from chemical knowledge or intuition, an addition that the Dewar methods consider essential. The human researcher knows for which molecules it is necessary to obtain the best fit. For instance, it is useless to obtain parameters for carbon and hydrogen that describe the properties of cubane correctly if the results for benzene are significantly different from experiment. An attentive and knowledgeable chemist can also guide the search into areas of the parameter hypersurface that make sense as far as the absolute magnitude of the parameters themselves are concerned. As with many chemical properties, the parameter values should vary periodically. While this should not unduly constrain the final values, parameters should follow well-defined general trends for proper interaction with other elements. In terms of the actual NDDO model, the actual parameters allowed to vary in the two methods are quite different. In AM1, a large number of values we used from spectroscopy for some of the one-center terms and the other parameters derived with these values fixed. (This is possible only for the lighter elements in the Main Group.) PM3 allowed ALL of these values to float, resulting in substantially more parameters. AM1 also had a quite different concept as to the application of the Guassian functions introduced with AM1 to adjust the core-electron/core- electron repulsion function. Workers in the Dewar group and subsequently in my group see Gaussian functions as PATCHES to the theory, not integral parts. All models fail at some point and the Gaussians were introduced to help with some of the systematic errors in MNDO. Traditionally, these patches were applied to adjust for difficult molecular systems AFTER semiempirical parameters were stabilized. PM3 includes these Gaussian functions (two for each element) FROM THE BEGINNING. Our experience indicates that in such a situtaion, the chemistry os the element will very likely be very strongly effected by the presence of these functions and the importance of the "real", "chemical" parameters will be reduced and swallowed up bu the Gaussians. In short, Gaussians should only be used where absolutely needed, and then viewed with askance. The essence of the difference between the two philosophies is evident: the theoretical basis for the method is either accepted or denied. Significant approximations are made to gain the speed advantage that semiempirical methods enjoy over their ab initio quantum mechanical brethren. But both the ab initio and semiempirical models are based on the Hartree-Fock set of ideas. These ideas possess theoretical rigor as regards solution of the Schrodinger Equation. If one simply views the semiempirical parameters as adjustables within a curve-fit scheme rather than as components of a theoretical model, little faith or importance resides in the meaning of their final values. Simply put, the method of parameterization described above and used so successfully with AM1 and MNDO (and now SAM1) expresses confidence in the theory. With a firmer footing in chemical reality, AM1 parameters are more likely to yield useful results for situations not specifically included in the molecular basis set for parameterization (MBSP). Some Practical Considerations ----------------------------- The differences in errors between the two methods as published are minimal, but that does not relate the real story of how the methods perform differently. Some key points: - PM3 is clearly better for NO2 compounds as a larger number of these were included in the MBSP. - PM3 is usually a little better for geometries, as these were also heavily weighted. - The molecular orbital picture with PM3 is usually different from that expected or that predicted by other methods. This is a direct consequence of the lack of attention paid to the absolute values of Uss and Upp. It can be seen in the lack of performance in ionization potentials. - PM3 charges are usually unreliable, again a result of the rather strange values that some of the parameters take on, even when other experimental data such as heats of formation and geometries are acceptable. This makes PM3 essentially useless for the derivation of molecular m echanics force fields. Perhaps the best known example of this is the case of formamide. The partial charges for the atoms in the molecules are listed below. The lack of any appreciable charge on N has led to a reversal of the actual bond dipole between C and N in this molecule! Atom AM1 PM3 HF/6-31G* --------------------------------------------- O -0.3706 -0.3692 -0.5541 C 0.2575 0.2141 0.5079 N -0.4483 -0.0311 -0.8835 O // H-C \ NH2 - Several papers have been published describing the performance of AM1 vs. PM3: Dewar, M. J. S.; Healy, E. F.; Yuan, Y.-C.; Holder, A. J. J. Comput. Chem. 1990, 11, 541. Smith, D.A. J. Fluor. Chem. 1990, 50, 427 Smith, D.A.; Ulmer, C.W.; Gilbert, M.J. J. Comput. Chem. 1992, 13, 640. - Most reserachers in my experience have stopped using PM3 and have returned to AM1. An Example of Parameterization Values for Aluminum -------------------------------------------------- Parameter AM1 MNDO PM3 Uss, eV -24.353585 -23.807097 -24.845404 Upp, eV -18.363645 -17.519878 -22.264159 zetas, au 1.516593 1.70288 } 1.444161 zetap, au 1.306347 1.073269 betas, eV -3.866822 -0.594301 } -2.670284 betap, eV -2.317146 -0.956550 alpha 1.976586 1.868839 1.521073 Gaussians: Intensity #1, eV 0.090000 - -0.473090 Width #1 12.392443 - 1.915825 Position #1 2.050394 - 1.451728 Intensity #2, eV - - -0.154051 Width #2 - - 6.005086 Position #2 - - 2.51997 The point on the potential surface located by PM3 is significantly different than that located by AM1. This is immediately apparent from the large discrepancy between the Upp values. These are the important one- electron energy values and they have strong influence on the parameter hypersurface. Also, the difference between Uss and Upp for both MNDO and AM1 is about 6 eV. This has been reduced to 2.5 eV in PM3. The real difficulty, however, is in the Beta values. These parameters are the two-center/one- electron resonance terms and are responsible for bonding interactions between atoms. The PM3 values are almost zero, resulting in the conclusion that there is very little bonding between atoms involving aluminum! (Note that the AM1 values for betas and betap spread out around the single MNDO value for beta. This suggests that the MNDO values were reasonable and AM1 adds greater flexibility.) PM3 regains the bonding interactions lost in the low beta values with two strongly attractive Gaussians spanning the bonding region. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=