QcWf[4.oVK@ `} grnx9lgKň@R4 oAbn)6z7uXM^@0U%+ %*۷ <`H\vGv:{uWjIn Bl\瘖sn@pi_7cek 9\CFrnndrwƏYy5;Md5bѬ4) dɸ Aw,R[ f3@t\＂л q,keocq{cg=u${U+tRZБz(\d.xSQ)t,Xd$[ yj pɲ-V%q)T}ӹA{eWT^"^ ⧉z 3qABLyU, Աgb+GS//4Ae6Bw=tvŤV3в5@g8B<,z9*[XP/Ip[ša5D=vڤam쩜1ɮ;RMQdwq$VMCDrb2 C>#AX!2 )xOz.Uh9gY&>p (4(PW}Ȏ@L܈z6^Qk@v|#.ԏ.8Ďo5`~obd)L0Pp ` $QqD3wk(:êtXgwY4Ԧ-L}ixa&ݩO^\_e2Wh*ȖdWc _> Q*weI g1Pjo#oQzCN`ɑV?v%Ѫk[`'wf+#W Ҙ&R"+g>þݸA}e~2rЉHtWf{82} u^ -t0;_(8 {J uCq4xN<^7;0<-m;X#Qqtm?[)SϤPJ{I-3&oJ(~hBLk&W|f "}"Vʇv #BbD>pϙ5j/~qwpUfqٮ,H䝨c 6{,A\o"^Q`97J`fd99cf1g~l6Xj:@VvUoDZ6Ukݕs^knʰ"b&GԾÒsV#L5eaVڌZl="2pE)_W^VqLi1D~ AݐeMg(_7#xo!D8L >}|ȗTfwA69,jnA„B'>m0l­!"˿pw$c ѝ>?ƣ'̆Ԍ㧾q!΃9-7Wy79[uTVYOLPX]z{m_ (]_G'>`&[ģwz* nuDH!өX{yx@.OarO?PON؏From qibvigap@lg.ehu.es Thu Sep 19 06:28:02 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by infomeister.osc.edu (8.7.5/950822.1) id FAA25838; Thu, 19 Sep 1996 05:26:45 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA25349; Thu, 19 Sep 96 11:26:12 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA15803; Thu, 19 Sep 1996 11:33:33 +0100 Date: Thu, 19 Sep 1996 11:33:33 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: chemistry@infomeister.osc.edu Subject: G: References about pyrazinium,... calculations In-Reply-To: <199609181954.AA22412@uscmail.usc.es> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Fellows: I am looking for published work about the charge distribution in the protonated cations pyrazinium, pyridazinium and pyrimidinium, done with Gaussian (or another SCF software) at any level of approximation (the highest, the best, of course...). And realted to this, I have another question: Are the point charges calculated with Extended Huckel or semiempirical methods (MINDO, MNDO, AM1, PM3,...) reliable (enough)? Thank you very much -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From jsl@virgil.ruc.dk Thu Sep 19 10:28:03 1996 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by infomeister.osc.edu (8.7.5/950822.1) id JAA01375; Thu, 19 Sep 1996 09:57:14 -0400 (EDT) Received: from virgil.ruc.dk by emma.ruc.dk (4.1/JBA-1.18) id AA08237; Thu, 19 Sep 96 16:01:19 +0200 Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 19 Sep 96 15:54:51 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 19 Sep 96 15:54:47 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@infomeister.osc.edu Date: Thu, 19 Sep 1996 15:54:44 +0100 Subject: CCL: Molecular Plots Priority: normal X-Mailer: Pegasus Mail for Windows (v2.23) Message-Id: <15167011B61@virgil.ruc.dk> CCL: In connection with some work in the field of semiempirical all-valence-electrons LCAO theory I wish to plot a 3-dimensional function corresponding to a weigthed sum of the AO densities: --- \ 2 F(x,y,z) = > W Phi (x,y,z) / i i --- i The sum is over AOs i in the basis set, W are the weight factors, and Phi the AO wavefunctions (e.g., STOs). Is there any software available for conveniently producing contour maps etc. of a function of this type? Thanks for any hints. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: JSL@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From mbdtsnm@hpf.ch.man.ac.uk Thu Sep 19 11:28:09 1996 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by infomeister.osc.edu (8.7.5/950822.1) id LAA01862; Thu, 19 Sep 1996 11:21:21 -0400 (EDT) Received: from hpf.ch.man.ac.uk (actually mchhpf.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Thu, 19 Sep 1996 16:21:05 +0100 Date: Thu, 19 Sep 1996 16:21:00 +0100 Message-Id: <18838.9609191521@hpf.ch.man.ac.uk> From: "Nathaniel (noj) Malcolm" To: jsl@virgil.ruc.dk Cc: chemistry@infomeister.osc.edu In-Reply-To: <15167011B61@virgil.ruc.dk> (message from Jens Spanget-Larsen on Thu, 19 Sep 1996 15:54:44 +0100) Subject: Re: CCL:Molecular Plots you should be able to use the standard utility gnuplot to lookat contours, as long as you can output slices of your data.......i have defintely used it for plot psi^2 contours......but some years ago noj From andy@neptune.chem.uga.edu Thu Sep 19 11:38:00 1996 Received: from neptune.chem.uga.edu for andy@neptune.chem.uga.edu by infomeister.osc.edu (8.7.5/950822.1) id KAA01605; Thu, 19 Sep 1996 10:30:27 -0400 (EDT) Received: (from andy@localhost) by neptune.chem.uga.edu (8.7.4/8.7.3) id KAA13279 for chemistry@infomeister.osc.edu; Thu, 19 Sep 1996 10:31:43 -0400 Date: Thu, 19 Sep 1996 10:31:37 -0400 (EDT) From: Andy Dustman Sender: andy@neptune.chem.uga.edu To: chemistry@infomeister.osc.edu Subject: G: Unrecognized representation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII While performing the final population analysis, G94 (Rev C.3) reports: Unable to determine electronic state: unrecognized representation Here is the input file: # MP2/6-31+G* opt=(addredundant,calchffc) nosymm propenoate, rotation of carboxylate -1 1 C 0.00000 0.00000 0.0 C 1.49060 0.00000 0.0 C 2.19505 1.14001 0.0 O -0.62364 1.04495 0.0 O -0.68580 -1.18576 0.0 H 3.29686 1.11914 0.0 H 1.70087 2.12431 0.0 H 2.00276 -0.97621 0.0 3 2 1 4 0.0 S 6 30.0 After 180 deg of rotation, the point group should again be Cs but G94 reports C1. (In fact, it should be indistinquishable from the original structure.) The initial population reports an 1-A' electronic state. Obviously there is some problem with the symmetry. When I initially ran this job, it was without the NOSYMM keyword, and it failed shortly after starting the second conformation because of the point group change from Cs to C1. With NOSYMM it at least computed all of the structures, though it did not produce exactly the requested dihedral angle (usually -0.00005 deg off). What is the "correct" way of avoiding these symmetry problems in G94? As usual, I will try to post a summary. Andy Dustman / Computational Center for Molecular Structure and Design / UGA ===== For PGP public key: finger andy@neptune.chem.uga.edu | pgp -fka ===== Sure, the Telecomm Act will create jobs: 100,000 new thought-cops on the net http://charon.chem.uga.edu/~andy mailto:andy@CCMSD.chem.uga.edu <}+++< From rgab@mx.trpntech.com Thu Sep 19 12:28:02 1996 Received: from mx.trpntech.com for rgab@mx.trpntech.com by infomeister.osc.edu (8.7.5/950822.1) id MAA02249; Thu, 19 Sep 1996 12:20:07 -0400 (EDT) Message-ID: Date: 19 Sep 1996 09:17:30 -0700 From: "Richard Bone" Subject: Floppy Molecules To: "CCL" X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Floppy Molecules Apologies for coming into this late in the day. There is a fairly large literature on "floppy" or "non-rigid" molecules. I think that the already-mentioned reference to Bunker's book "Molecular Symmetry and Spectroscopy" covers the most important work in the field. But there is much else. 2 references I have to hand are: H. Frei, A. Bauder, H. H. Gunthard, "The Isometric Group of Nonrigid Molecules", in Top. Curr. Chem., Vol. 81, Large Amplitude Motion in Molecules, I, p3, (1979) "Symmetries and Properties of Non-Rigid Molecules", Ed. J. Maruani and J. Serre, Studies in Physical and Theoretical Chemistry, 23, Elsevier, Amsterdam, (1982). There is also a recently published book-volume edited by Yves Smeyers "Structure and Dynamics of Non-Rigid Molecular Systems", Kluwer, 1994, in which I have an article with some perspectives on how to treat the problem of inter- conversions between minima of different geometries/symm- etries. One small point on the use of the term "fluxional": I have also seen it used to refer to inorganic molecules where no valence tautomerisation occurs, the archetypal example of which is PF_5. The Smith-Berry internal rotation which interconverts all the indistinguishable Trig-bipy isomers doesn't change any bonding very much. Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Terrapin Technologies, Inc. 750-H Gateway Blvd. South San Francisco CA 94080-7020 USA Tel. +1 (415) 244 9303 FAX +1 (415) 244 0705 E-mail rgab@trpntech.com http://www.sosei.com/Companies/Terrapin.html From owner-chemistry@osc.edu Thu Sep 19 13:28:03 1996 Received: from bedrock.osc.edu for owner-chemistry@osc.edu by infomeister.osc.edu (8.7.5/950822.1) id NAA02519; Thu, 19 Sep 1996 13:14:09 -0400 (EDT) Received: from cliff.acs.oakland.edu for bbesler@ouchem.chem.oakland.edu by bedrock.osc.edu (8.7.6/950822.1) id NAA09235; Thu, 19 Sep 1996 13:14:09 -0400 (EDT) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.7.6/8.7.3) with SMTP id NAA16354 for ; Thu, 19 Sep 1996 13:15:30 -0400 (EDT) Received: by ouchem.chem.oakland.edu; id AA08019; Thu, 19 Sep 1996 13:15:06 -0400 From: "Brent H. Besler" Message-Id: <9609191715.AA08019@ouchem.chem.oakland.edu> Subject: Best File Format for Submission of Pictures to Journals? To: chemistry@osc.edu Date: Thu, 19 Sep 1996 13:15:06 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit What is the best picture format to use for electronic submission to journals among GIF, JPEG, and TIFF? I would like to preserve as much resolution as possible when scaling the picture size. From owner-chemistry@osc.edu Thu Sep 19 14:28:03 1996 Received: from bedrock.osc.edu for owner-chemistry@osc.edu by infomeister.osc.edu (8.7.5/950822.1) id NAA02917; Thu, 19 Sep 1996 13:38:06 -0400 (EDT) Received: from csiat1.tij.uabc.mx for siatij@csiat1.tij.uabc.mx by bedrock.osc.edu (8.7.6/950822.1) id NAA09719; Thu, 19 Sep 1996 13:38:06 -0400 (EDT) Message-Id: <199609191738.NAA09719@bedrock.osc.edu> Received: by csiat1.tij.uabc.mx (1.38.193.5/16.2) id AA03137; Thu, 19 Sep 1996 13:30:45 -0400 Date: Thu, 19 Sep 1996 13:30:45 -0400 From: Usuario generico de internet To: chemistry@osc.edu Subject: investigacion Quisieramos mas informacion sobre los mecanismos de cuantificacion del grupo de los alcoholes . Favor de mandar a la direccion siguiente: siatij@csiat1.uabc.tij.mx y en asunto investigacion Aclaracion es buzon general From nash@chem.wisc.edu Thu Sep 19 16:28:04 1996 Received: from wisc.edu for nash@chem.wisc.edu by infomeister.osc.edu (8.7.5/950822.1) id PAA03690; Thu, 19 Sep 1996 15:43:20 -0400 (EDT) Received: by wisc.edu; id AA19401; 5.57/37; Thu, 19 Sep 96 14:52:13 -0500 Message-Id: <9609191952.AA19401@wisc.edu> X-Sender: jrnash@students.wisc.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Sep 1996 14:45:03 -0500 To: "Brent H. Besler" From: "John R. Nash" Subject: Re: Best File Format for Submission of Pictures to Journals? Cc: CHEMISTRY@infomeister.osc.edu At 01:15 PM 9/19/96 -0500, you wrote: >What is the best picture format to use for electronic submission to >journals among GIF, JPEG, and TIFF? I would like to preserve as much >resolution as possible when scaling the picture size. I talked to a friend who works at a chemistry journal, and she said: --- The best is an .eps file. A tiff file is a bitmapped (for a scanned) file and is more likely to cause problems w/ scaling. --- I know that JPEG is a "lossy" format, losing some data for the purpose of making smaller files. This is good for web pages, but bad for submissions. GIF doesn't lose information, but is bitmapped like TIFF, I believe. EPS (or just plain PostScript) is probably the best bet if possible. In general, any "vectorized" format will scale better than a "bitmapped" one. PICT is probably ok as well, since it usually contains vectorized data. -john -==-John R. Nash-==-nash@chem.wisc.edu-==- From stefan@indi.aci.uni-heidelberg.de Thu Sep 19 19:28:06 1996 Received: from relay.urz.uni-heidelberg.de for stefan@indi.aci.uni-heidelberg.de by infomeister.osc.edu (8.7.5/950822.1) id SAA04730; Thu, 19 Sep 1996 18:46:52 -0400 (EDT) Received: from sun0.urz.uni-heidelberg.de (sun0.urz.uni-heidelberg.de [129.206.100.126]) by relay.urz.uni-heidelberg.de (8.7.5/8.7.4) with SMTP id AAA25317 for ; Fri, 20 Sep 1996 00:46:50 +0200 (MET DST) Received: from indi.aci.uni-heidelberg.de by sun0.urz.uni-heidelberg.de (SMI-8.6/SMI-SVR4) id AAA28131; Fri, 20 Sep 1996 00:46:48 +0200 Received: by indi.aci.uni-heidelberg.de (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.osc.edu id AAA01728; Fri, 20 Sep 1996 00:50:30 +0200 From: "Stefan Beyreuther" Message-Id: <9609200050.ZM1726@indi.aci.uni-heidelberg.de> Date: Fri, 20 Sep 1996 00:50:30 -0600 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: CHEMISTRY@infomeister.osc.edu Subject: SUMMARY: Wilson Out-Of-Plane Coordinate Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers A week ago I asked the following question: > Could someone explain me what exactly the Wilson out-of-plane > coordinate is? > > It is used in forcefields like CFF91 or ESFF (Discover, MSI). > The functional form is > > ___ > \ ' 2 > > K X > /__, i > i > > > The manual only says: > > "The functional form of the out-of-plane energy ..., where the > coordinate is an average of the three possible angles associated > with the out-of-plane center. The single parameter that is > associated with the central atom is a fit quantity." > > I have the corresponding reference > > Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations, > Dover, New York (1980). > > but we don't have the book here. The answers I received are appended. Thanks a lot folks. Stefan Stefan Beyreuther Anorganisch-Chemisches Institut fon +49-6221-548634 Universitaet Heidelberg fax +49-6221-545707 69120 Heidelberg e-mail stefan@indi.aci.uni-heidelberg.de Germany On Sep 10, 6:41pm, Ernst U. Wallenborn wrote: > Subject: Re: CCL:Wilson Out-Of-Plane Coordinate > > Hi, > > > i think you are referring to what is called term (4) > of the cvff91 forcefield in the Discover manual. > Wilson, Decius and Cross say: > > -----quote----- > 3 1" > / theta ` > / ` > 1------4 phi_1 1-------4----------2,3 > \ > \ > 2 > > The basic definition of the angle involved may be given as > > e_42 x e_43 > sin theta =---------------- * e_41 > sin phi_1 > -----unquote----- > > i.e. the angle is defined as the one between the bond and the plane > formed by the three other atoms. Since there are three posssibilities > to choose (atoms 1, 2, 3) Discover takes an average and uses this > for the calculations. > > Hope this helps > > > -- > Ernst-Udo Wallenborn > Laboratorium fuer Physikalische Chemie > ETH Zentrum > CH-8092 Zuerich > >-- End of excerpt from Ernst U. Wallenborn On Sep 10, 12:42pm, Peter Shenkin wrote: > Subject: CCL:Wilson Out-Of-Plane Coordinate > On Sep 10, 4:29pm, Stefan Beyreuther wrote: > > Subject: CCL:Wilson Out-Of-Plane Coordinate > > Could someone explain me what exactly the Wilson out-of-plane > > coordinate is? > > If A, B and C are connected to a common "central" atom, D, then > the angle that the AD vector makes with the BDC plane is a Wilson > angle. The angle that the BD vector makes with the ADC plane > is another one. > > MMFF (Tom Halgren's Merck Molecular Force Field) also uses these. > > -P. > > -- > ****** ********** In Memoriam, Bill Monroe, 1911 - 1996 ****************** > * Peter S. Shenkin, Chemistry, Columbia U., 3000 Broadway, Mail Code 3153,* > ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** > MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html > >-- End of excerpt from Peter Shenkin On Sep 11, 10:32am, Tom Sundius U of Helsinki +358 0 1918339 wrote: > Subject: CCL:Wilson Out-Of-Plane Coordinate > > > Could someone explain me what exactly the Wilson out-of-plane > > coordinate is? > ... > > I have the corresponding reference > > > Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations, > > Dover, New York (1980). > > but we don't have the book here. > > Another reference, which may be very helpful, is > S. Califano: Vibrational States, J. Wiley & Sons, London (1976) > ISBN 0-471-12996-8 (there may be a new edition of this useful book) > Chapter 4 of this book deals with the Wilson internal coordinates. > > Sometimes the out-plane bend coordinate is also defined as "impromper > torsion" which involves the dihedral angle between two adjoining planes. > The difference between the two definitions is, however, insignificant for > an (almost) planar configuration. > > +-----------------------------------------------------------------------+ > ! Tom Sundius, Dept. of Physics Internet: Tom.Sundius@Helsinki.fi ! > ! University of Helsinki, Finland sundius@phcu.helsinki.fi ! > +-----------------------------------------------------------------------+ > >-- End of excerpt from Tom Sundius U of Helsinki +358 0 1918339 From guojx@infoc3.icas.ac.cn Thu Sep 19 20:28:04 1996 Received: from infoc3.icas.ac.cn for guojx@infoc3.icas.ac.cn by infomeister.osc.edu (8.7.5/950822.1) id UAA04969; Thu, 19 Sep 1996 20:04:29 -0400 (EDT) Received: (from guojx@localhost) by infoc3.icas.ac.cn (8.6.9/8.6.9) id HAA01091; Fri, 20 Sep 1996 07:39:05 +0800 Date: Fri, 20 Sep 1996 07:39:04 +0800 From: Guo Jian-xin Subject: Re: CCL:G:G: Unrecognized representation To: Andy Dustman cc: chemistry@infomeister.osc.edu In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Andy Dustman, I have meet the same problem in run Gaussian92, this problem can be resolved by using the virtual atoms to define the molecular inneral coordination . Good luck. Guo