From owner-chemistry@ccl.net Mon Jul 8 08:59:08 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id IAA02364; Mon, 8 Jul 1996 08:50:56 -0400 (EDT) Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by bedrock.ccl.net (8.7.5/950822.1) id IAA25675; Mon, 8 Jul 1996 08:50:54 -0400 (EDT) Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id KAA09746; Mon, 8 Jul 1996 10:20:45 -0230 Date: Mon, 8 Jul 1996 10:20:45 -0230 (NDT) From: Uli Salzner To: ccl Subject: IPs of organic compounds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, is there a catalog of photoelectron spectra? I am calculating IPs and need experimental data for comparison. I am interested in organic pi-systems. I would be very grateful for hints where I can find those data. Thanks in advance, Ulrike Salzner Department of Chemistry Memorial University of Newfoundland St. Johns, NF A1B 2N5 Canada Tel.: (709) 737-2151 Email:uli@smaugs.physics.mun.ca From THORSTEN.LOEHL@DENOTES.henkel.de Mon Jul 8 10:59:12 1996 Received: from CPO.HENKEL.DE for THORSTEN.LOEHL@DENOTES.henkel.de by www.ccl.net (8.7.5/950822.1) id KAA02891; Mon, 8 Jul 1996 10:19:15 -0400 (EDT) From: X400-Originator: THORSTEN.LOEHL@DENOTES.henkel.de X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=HENKEL/ADMD=DBP/C=DE/;0006700002107730000004] X400-Content-Type: P2-1988 (22) Priority: Urgent Message-ID: <0006700002107730000004*@MHS> To: "internet,":;@www.ccl.net, "chemistry(a)www.ccl.net" Subject: Detergent - modeling //08.07.96 15:13:46 Date: Mon, 8 Jul 1996 16:16:40 +0100 Hallo everybody, being in loose touch with computational chemistry for some time I have recently asked myself if there have already been efforts to understand the behaviour of detergents in solution. A typical type of detergent would be a long-chain alcohol group (C8-C18) with a number of 3-10 ethylenoxides added to it. Is there anyone aware of published work? If so, I would like to ask to respond to my email address. I promise to sum the results for everybody. Thank you Thorsten Loehl, Henkel KGaA, Duesseldorf, Germany Email: Thorsten.Loehl@henkel.de From owner-chemistry@ccl.net Mon Jul 8 11:59:15 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id LAA03317; Mon, 8 Jul 1996 11:30:27 -0400 (EDT) Received: from alef.in.irb.hr for kiralj@olimp.irb.hr by bedrock.ccl.net (8.7.5/950822.1) id LAA28252; Mon, 8 Jul 1996 11:30:24 -0400 (EDT) From: Received: from olimp.irb.hr (olimp.irb.hr [161.53.128.17]) by alef.in.irb.hr (8.7.5/8.7.3) with SMTP id RAA07509 for ; Mon, 8 Jul 1996 17:30:16 +0200 (MET DST) Received: by olimp.irb.hr (MX V4.1 VAX) id 21; Mon, 08 Jul 1996 17:30:14 MET-DST Date: Mon, 08 Jul 1996 17:30:13 MET-DST To: CHEMISTRY@ccl.net Message-ID: <009A507B.959CF724.21@olimp.irb.hr> Subject: ASTER DATABASE Hi Netters, Does anybody know the ASTER data base (AScessment Tools for the Evaluation of Risk. US-EPA Duluth, MN)? I know it is a database for physicalchemical properties. I don't have any idea on how to get onto there and extract data. I appreciate any suggestion of help. Thanks in advance Rudolf -------------------- Rudolf Kiralj X-ray Laboratory, Department of Materials Science and Electronics Rudjer Boskovic Institute Bijenicka 54, P.O.B. 1016 Hr-10001 Zagreb, Croatia e-mail: kiralj@olimp.irb.hr From Darren.Andrews@man.ac.uk Mon Jul 8 12:59:24 1996 Received: from nessie.mcc.ac.uk for Darren.Andrews@man.ac.uk by www.ccl.net (8.7.5/950822.1) id MAA03784; Mon, 8 Jul 1996 12:45:43 -0400 (EDT) Received: from [129.11.12.179] (actually chmibm104.leeds.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 8 Jul 1996 17:44:52 +0100 X-Sender: mbcdpa@130.88.200.20 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 Jul 1996 17:48:45 +0100 To: chemistry@www.ccl.net From: Darren.Andrews@man.ac.uk (Darren Andrews) Subject: Molecule Viewer for MACs Does anybody know of a (preferrably cheap) viewer for MAC's for the output files of Ab Initio type programs like Gaussian, GAMESS, Cadpac etc. I know it's probably asking for too much for a program that will view all types. I know Spartan is quite good for Gaussian but won't do anything else. Cheers. Darren Andrews. University of Leeds, School of Chemistry, Leeds. LS2 9JT. England. Darren.Andrews@man.ac.uk PGP: 512/62A971A9 Tel: 0113 233 6469. Fax: 0113 233 6565. From jvasquez@ewu.edu Mon Jul 8 13:59:23 1996 Received: from owl.ewu.edu for jvasquez@ewu.edu by www.ccl.net (8.7.5/950822.1) id NAA04311; Mon, 8 Jul 1996 13:54:01 -0400 (EDT) Received: from [146.187.64.147] (ewu65491.ewu.edu) by ewu.edu (PMDF V5.0-5 #9372) id <01I6TT0CQBXC02U7JH@ewu.edu> for chemistry@www.ccl.net; Mon, 08 Jul 1996 10:53:02 -0800 (PST) Date: Mon, 08 Jul 1996 10:52:41 -0800 From: jvasquez@ewu.edu (John Vasquez) Subject: volumes of ion-water complexes` X-Sender: jvasquez@eagle.ewu.edu To: chemistry@www.ccl.net Message-id: X-Envelope-to: chemistry@www.ccl.net MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT I am currently working on creating a theoretical model to predict the partial molar volumes and molecular features corresponding to ion-water complexes. To do this, I need to calculate the volume of the ion-water complex itself...Is anyone aware of any publications on calculating these volumes? If any are found, please e-mail them to me. Thank you very much. John Vasquez jvasquez@ewu.edu From dominik@rchsg9.chemie.uni-regensburg.de Mon Jul 8 14:02:04 1996 Received: from comsun.rz.uni-regensburg.de for dominik@rchsg9.chemie.uni-regensburg.de by www.ccl.net (8.7.5/950822.1) id MAA03654; Mon, 8 Jul 1996 12:27:26 -0400 (EDT) Received: from rchsg9.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA04844 (5.65c/IDA-1.4.4 for ); Mon, 8 Jul 1996 18:27:11 +0200 Received: by rchsg9.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for chemistry@www.ccl.net) id AA25857; Mon, 8 Jul 96 18:27:55 +0200 From: "Dominik Horinek" Message-Id: <9607081827.ZM25855@rchsg9.chemie.uni-regensburg.de> Date: Mon, 8 Jul 1996 18:27:55 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: CCL:MCSCF active space selection Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear Netters: I need accurate ground state energies for the HOCl molecule in regions of the potential energy surface far away from the equilibrium geometry. I tried CASSCF with the D95+* basis set using Gaussian94. With every set of CAS-orbitals the calculation was aborted due to a wrong active space, I got warnings like: "large rotation I, J ..." with I and J variing over the full range of MO's. In my calculation the active space should consist of all orbitals which are affected by a special distorsion, say the cleavage of the Cl-O bond, but choosing those orbitals results in the errors cited above. After a look at the molecular orbital coefficients it seems to me that the only complete active space consists of all orbitals. Any suggestions how to select a right active space in this case? I would be glad to receive additional pointers to introductory texts on MC-SCF. Thanks in advance, Dominik P.S.: I already searched the CCL archive but found nothing really apropriate. -- ------------------------------------------------------------------ Dominik Horinek Institut fuer physikalische und theoretische Chemie Lst. Prof. Dick Universitaet Regensburg Universitaetsstr. 31 93053 Regensburg Deutschland email: Dominik.Horinek@chemie.uni-regensburg.de ------------------------------------------------------------------ From Matthew.Harbowy@unilever.com Mon Jul 8 14:59:18 1996 Received: from gatekeeper.homecare.com for Matthew.Harbowy@unilever.com by www.ccl.net (8.7.5/950822.1) id OAA04487; Mon, 8 Jul 1996 14:11:34 -0400 (EDT) Received: from x500mhub.lo.u1388.unilever.com by gatekeeper.homecare.com; (5.65v3.2/1.1.8.2/24Jan95-0439PM) id AA04331; Mon, 8 Jul 1996 19:11:00 +0100 Received: by x500mhub.lo.u1388.unilever.com; Mon, 8 Jul 96 18:58:53 Z X400-Received: by /c=GB/admd=telemail/prmd=Unilever/; Relayed; 08 Jul 96 18:58:44 Z X400-Received: by mta MTAunilever in /c=GB/admd=telemail/prmd=Unilever/; Relayed; 08 Jul 96 18:58:44 Z X400-Mts-Identifier: [/c=GB/admd=telemail/prmd=Unilever/; 0543231E14C5403A-MTAunilever] Content-Identifier: 0543231E14C5403A Content-Return: Allowed X400-Content-Type: P2-1988 ( 22 ) Conversion: Allowed Priority: normal Disclose-Recipients: Prohibited Alternate-Recipient: Allowed X400-Originator: Matthew.Harbowy@unilever.com X400-Recipients: non-disclosure; Message-Id: <0543231E14C5403A*/c=gb/admd=telemail/prmd=unilever/o=unilever/ou=ccmail/s=Harbowy/g=Matthew/@MHS> Date: 08 Jul 96 18:58:44 Z From: "Matthew Harbowy" To: "chemistry@www.ccl.net" (Return requested) (Receipt notification requested) Return-Receipt-To: "Matthew Harbowy" Subject: Wht usually goes wrong: my experience with MOPAC Seeing some messages on minimization problems with negative frequencies of late here, I thought I'd add some of my experiences. 1. Bad geometry choices: frequently, a bad choice of geometry definition, or worse, forcing an artificial symmetry either through bad z-matrix definition or through actual symmetry constraints, causes one to minimize to a hilltop or hillside while one's gradients happily descend to near zero. At least with MOPAC 6, and perhaps with other MOPAC's, gradients are determined from the z-matrix definition of coordinates, and if a particularly shallow twist is defined along the coordinates, while there is an (undefined) twist that is steep, you could spend a lot of computation hours in small changes in geometry that ignore the larger gradients present and fail to completely minimize the molecule. It would probably be worse for graphical-interfaces where you have little to no control over such failures. Ways to resolve: use a different minimizer, or even try XYZ to minimize in cartesian space. Or, set the gradient to minimize further than you currently are. Or: try a different program. Sometimes the cure is to see if you can repeat it on another machine or program. 2. failure to minimize: sometimes you think you've minimized enough, but you do something inadvertant that messes that up. Most programs are smart enough to make sure that you have not been subject to bizarre rounding errors, but sometimes it makes sense to double check everything. Bond angles near 180 degrees can be the biggest headache, and it is conceivable that a rounding error might cause large geometry changes. Ways to resolve: check the geometry after minimization, and before and after frequency calcs. Also, make sure you haven't invoked a series of keywords that cancel one another or set different minimization defaults. Another big bad example (in ab-initio, not mopac) is minimizing in one basis set, and then doing a freq calc in another. There's nothing stopping a novice in principle from minimizing in MM2, ie, in Hyperchem, then using a single point calculation to print frequencies in AM1. That's probably a big error. I realize many, if not most, of the people here are not novices. But perhaps we should, in true internet style, have a faq on such things! -matt From dsmith@dasgroup.com Mon Jul 8 15:59:13 1996 Received: from pop.third-wave.com for dsmith@dasgroup.com by www.ccl.net (8.7.5/950822.1) id PAA04986; Mon, 8 Jul 1996 15:24:23 -0400 (EDT) Received: from dirac ([206.31.47.72]) by pop.third-wave.com (Netscape Mail Server v1.1) with SMTP id AAA13987 for ; Mon, 8 Jul 1996 15:21:36 -0400 X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) To: CHEMISTRY@www.ccl.net From: dsmith@dasgroup.com (Doug Smith) Subject: MOPAC vibrations negative for a ground state? Date: Mon, 8 Jul 1996 15:21:36 -0400 Message-ID: <19960708192136.AAA13987@dirac> Dear All: A question was recently posted from one of my co-workers, but there have been no satisfactory answers... indeed, most of the answers completely missed the point of the question. Let's try again, please. We have been examining (poly)nitrocubanes with and without other functional groups using MOPAC 93 and the PM3 Hamiltonian/parameters. Most structures optimize just fine, but a few give a very peculiar problem. The job in question, 1-amino-2-nitrocubane, was optimized using PM3 GEO-OK GNORM=0.01 PRECISE LET DDMIN=0.0 EF. The structure optimized using eigenvector following. SCF field was achieved with a GNORM of 0.00565. The jobs are run using the keywords: PM3 NODIIS GEO-OK GNORM=0.01 LET DDMIN=0.0 FORCE THERMO(273,1273) after the optimization has been completed. The gradient norm was 0.00545. The output from this force calculation gives a first root and first frequency of -296.6, which should indicate a transition structure. However, the program states that the "system is a ground state". The output follows: <--------------------------------------------------------------------------- ---------> Root No. 1 2 3 4 ............(etc.) 1 A" 2 A" 3 A" 1 A' ............ -296.6 78.2 191.1 203.4 ............ Description of Vibrations Vibration 1 1A" Atom Pair Energy Contribution Radial Freq. -296.56 N12 -- H14 27.5% 5.6% T-Dipole .3676 N12 -- H13 27.5% 11.3% Travel .1621 C 8 -- N12 7.6% .0% Red. Mass .4311 C 1 -- C 7 2.2% .0% System is a ground state <--------------------------------------------------------------------------- --------> Next, in order to try to understand this system and result, we reran just the force calculation in MOPAC 6.0 using the MOPAC 93 optimized geometry. The keywords for this run were: PM3 NODIIS GEO-OK GNORM=0.01 LET FORCE. We did not perform the thermodynamics calculation. The keyword DDMIN is not available in MOPAC 6.0. The gradient norm for this job was 0.16015. The output from this run gave root 1 as 17.68167 and the first printed vibrational frequency (number 2 - the first is not printed because it is less than 50) as 89.15. Obviously, this is not a transition structure. WHAT GIVES?!?!?!?! IS THIS A TRANSITION STRUCTURE OR A GROUND STATE (MINIMUM)??!?!?!?! Please reply to the list and we will monitor the answers and discussion. Thanks in advance. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology. From rosas@irisdav.chem.vt.edu Mon Jul 8 21:59:13 1996 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.7.5/950822.1) id VAA06724; Mon, 8 Jul 1996 21:44:47 -0400 (EDT) Received: by irisdav.chem.vt.edu (951211.SGI.8.6.12.PATCH1042/921111.SGI.AUTO) id VAA07075; Mon, 8 Jul 1996 21:36:31 -0700 From: "Victor M. Rosas Garcia" Message-Id: <9607082136.ZM7073@irisdav.chem.vt.edu> Date: Mon, 8 Jul 1996 21:36:27 -0400 In-Reply-To: dsmith@dasgroup.com (Doug Smith) "CCL:M:MOPAC vibrations negative for a ground state?" (Jul 8, 3:21pm) References: <19960708192136.AAA13987@dirac> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: dsmith@dasgroup.com (Doug Smith) Subject: Re: CCL:M:MOPAC vibrations negative for a ground state? Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everybody, I found the problem posted by Doug Smith very interesting. An excerpt follows. On Jul 8, 3:21pm, Doug Smith wrote: > Subject: CCL:M:MOPAC vibrations negative for a ground state? > The job in question, 1-amino-2-nitrocubane, was optimized using PM3 > GEO-OK GNORM=0.01 PRECISE LET DDMIN=0.0 EF. The structure optimized using > eigenvector following. SCF field was achieved with a GNORM of 0.00565. > > The jobs are run using the keywords: PM3 NODIIS GEO-OK GNORM=0.01 > LET DDMIN=0.0 FORCE THERMO(273,1273) after the optimization has been > completed. The gradient norm was 0.00545. The output from this force > calculation gives a first root and first frequency of -296.6, which should > indicate a transition structure. However, the program states that the > "system is a ground state". The output follows: > > <--------------------------------------------------------------------------- > ---------> > Root No. 1 2 3 4 ............(etc.) > 1 A" 2 A" 3 A" 1 A' ............ > -296.6 78.2 191.1 203.4 ............ > > Description of Vibrations > Vibration 1 1A" Atom Pair Energy Contribution Radial > Freq. -296.56 N12 -- H14 27.5% 5.6% > T-Dipole .3676 N12 -- H13 27.5% 11.3% > Travel .1621 C 8 -- N12 7.6% .0% > Red. Mass .4311 C 1 -- C 7 2.2% .0% > > System is a ground state > <--------------------------------------------------------------------------- > --------> > > Next, in order to try to understand this system and result, we reran > just the force calculation in MOPAC 6.0 using the MOPAC 93 optimized > geometry. The keywords for this run were: PM3 NODIIS GEO-OK GNORM=0.01 LET > FORCE. We did not perform the thermodynamics calculation. The keyword > DDMIN is not available in MOPAC 6.0. The gradient norm for this job was > 0.16015. The output from this run gave root 1 as 17.68167 and the first > printed vibrational frequency (number 2 - the first is not printed because > it is less than 50) as 89.15. Obviously, this is not a transition structure. > > WHAT GIVES?!?!?!?! > > IS THIS A TRANSITION STRUCTURE OR A GROUND STATE (MINIMUM)??!?!?!?! So I ran the job myself, using MOPAC93 R2 on an Indigo2Extreme, IRIX 5.3, CPU R4400. First, let's make sure I didn't screw up the compound, for some reason I'm never sure about my nomenclature. The molecule I used is: 2HN NO2 \____/ /_|__/| | |_|_| <-----This is supposed to be a cube! :) |/__|/ All the keywords were cut and pasted from the e-mail message to avoid typos or missing keywords. My results are as follows: ****************************************************************************** Gradient after geometry optimization: 0.0093 The point group was Cs. Gradient for the FORCE calculation: 0.02308 Roots: Root No. 1 2 3 4 5 6 7 8 1 A" 1 A' 2 A" 3 A" 2 A' 4 A" 3 A' 4 A' 18.4 155.4 178.8 207.8 292.4 304.8 403.3 434.5 [snip, snip] DESCRIPTION OF VIBRATIONS VIBRATION 2 1A' ATOM PAIR ENERGY CONTRIBUTION RADIAL FREQ. 155.41 C 1 -- N 9 8.1% (228.7%) 0.0% T-DIPOLE 0.5083 C 2 -- C 4 4.9% 0.1% TRAVEL 0.0892 N 9 -- H18 4.3% 17.7% RED. MASS 2.5416 N 9 -- H17 4.3% 17.7% [more snip, snip] ******************************************************************************** So I didn't get any imaginary freqs.! A few more details: I drew the molecule using PCMODEL v4.0 for SGI and used it to generate the Z-matrix for MOPAC after minimization with MMX. My only guess as to what could be the difference: * Check the revision of MOPAC93 that you are using. I'm using RELEASE 2. That could explain the difference between your MOPAC run and mine. * See if the imaginary freq you are getting corresponds to the rotation of the amino group (although in this case I don't know why the program would identify the molecule as a ground state). Hope this helps. Victor -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ----------------------------------------------------------------------- From mw@crystal.uwa.edu.au Mon Jul 8 22:59:13 1996 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.7.5/950822.1) id WAA06803; Mon, 8 Jul 1996 22:14:55 -0400 (EDT) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.6.11/8.6.9) with SMTP id KAA19201 for ; Tue, 9 Jul 1996 10:14:34 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA25360; Tue, 9 Jul 1996 12:08:03 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9607090209.AA00431@pack.crystal.uwa.edu.au> Subject: Van der Waals Radii! To: CHEMISTRY@www.ccl.net Date: Tue, 9 Jul 96 10:09:19 WST Mailer: Elm [revision: 70.85] Dear All, These are the replies I received regarding Van der Waals radii, * From Dr. Carlos H. Faerman: 'the reference I am aware of...is Acta Cryst. B41, 274 (1985).' *From Dr. Kober: 'I have not looked very hard recently, but as of a few years ago, these were the best I could find. I would appreciate it if you would let me know if you find more recent sources. S. C. Nyburg, et al. Acta Cryst B 1985, 41, 274 S. C. Nyburg, et al. Acta Cryst B 1987, 43, 106 D. Kirin Acta Cryst B 1987, 43, 405 Thank you to all those that replied, especially so promptly. I hope others have found this information as useful as I did. Magda Wajrak