From destack@unomaha.edu Sun Nov 16 16:33:32 1997 Received: from s-cwis.unomaha.edu for destack@unomaha.edu by www.ccl.net (8.8.3/950822.1) id QAA15416; Sun, 16 Nov 1997 16:17:59 -0500 (EST) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id PAA26454 for ; Sun, 16 Nov 1997 15:14:01 -0600 (CST) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 16 Nov 97 15:18:02 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 16 Nov 97 15:17:44 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 16 Nov 97 15:17:38 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BCF2A2.EDCD4DD0@zinc.unomaha.edu>; Sun, 16 Nov 1997 15:18:44 -0600 Message-ID: <01BCF2A2.EDCD4DD0@zinc.unomaha.edu> From: "Douglas E. Stack" To: "chemistry@www.ccl.net" Subject: Transition state search and link 9999 error Date: Sun, 16 Nov 1997 15:18:43 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable When trying to do a transition state search using the PM3 semi-empirical = method, the program always quits after one optimization cycle and gives = the following message: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad THERE'S SMALL CHOICE IN A BOWL OF ROTTEN APPLES. SHAKESPEARE Error termination request processed by link 9999. Error termination via Lnk1e in /disk2/gaussian/g94/l9999.exe. Job cpu time: 0 days 0 hours 14 minutes 0.9 seconds. File lengths (MBytes): RWF=3D 6 Int=3D 0 D2E=3D 0 Chk=3D 3 = Scr=3D 1 This happens using either OPT=3DTS with one structure or OPT=3DQST2 = using two structures. What's happening?? =20 Program : Gaussian 94: SGI-G94RevB.3 30-May-1995 13-Nov-1997 Douglas E. Stack=09 Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From elewars@alchemy.chem.utoronto.ca Sun Nov 16 18:33:31 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id SAA15734; Sun, 16 Nov 1997 18:18:34 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id SAA17184 for chemistry@www.ccl.net; Sun, 16 Nov 1997 18:18:32 -0500 (EST) Date: Sun, 16 Nov 1997 18:18:32 -0500 (EST) From: "E. Lewars" Message-Id: <199711162318.SAA17184@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: EXTENDED HUECKEL--SUMMARY AND THANKS VERY MUCH Sunday Nov 16 >From E. Lewars To: CCL Subj: Summary of Extended Hueckel Today--opinions This is a summary of the answers I got to my question (below). Thanks very much indeed to all who helped. ========= The Question (Wed 1997 Nov 12): Hello, What do people out there in netland think of the *current* status of the extended Hueckel method that was popularized by Roald Hoffmann, starting ca. 1963? It was, I think, the first generally applicable method, in the sense that it was not limited to planar pi electron arrays and could in principle perform geometry optimizations. Is it the general view that it is essentially obsolete, having been displaced by more sophisticated methods like MNDO and its decendants AM1 and PM3? Does it have some advantages over AM1 and PM3? Thanks E. Lewars ================ 1997 Nov 14 Summary of responses (I hope I haven't missed anyone): OPINIONS ON CURRENT STATE OF EHM #1 jsl@virgil.ruc.dk #2 fparnold@balihai.uchicago.edu #3 Alan.Shusterman@directory.reed.edu #4 Thomas Albright, U of Houston #1 13-NOV-1997 08:14:25.28 EHM does have one fundamental advantage over AM1, PM3 and other NDO-type theories: It is based on a proper treatment of atomic orbital (AO) overlap and thus includes terms that are neglected in NDO theories. For example, the repulsion between closed shells is a second order overlap effect, that is not reproduced by NDO theories. This leads to situations where EHM is superior to NDO theory. e.g., Tetrahedron 39, 3345 (1983). Jens Spanget-Larson, Roskilde U, Denmark ===== #2 12-NOV-1997 18:00:12.43 Personally, I find it still valuable, since it's generally consistent, includes support for elements that PM3, etc, don't, and has been generalized to the solid-state. It's also conceptually simple, serves as a good tool for a first pass at a problem, and is cheap to run, allowing qualitative results to be obtained for large systems in minimal time. If the limitations are taught first, it serves as an excellent tool for teaching basic modeling to students without overwhelming them in the technical details of ab-initio (or even better semi-empirical) methods. My preference, due to an interest in transition-metal systems, is to use Fenske-Hall, but that method is regrettably much less available, and has not been generalized to periodic systems. Fred P Arnold, Advanced Research Systems, Chicago == #3 Does it have some advantages over AM1 and PM3? --- end of quote --- EHMO has the obvious practical advantage of requiring far fewer parameters than either AM1 or PM3. Therefore, it has been extended to many more elements, and it is easier to "see" where the computed results come from in EHMO. The disadvantages of EHMO are many: one-electron method (no accounting of ee interactions or spin), can't predict energy differences, can't predict geometries (you say it can "in principle", but EHMO predicts that H2 should be a "superatom"). So its hard to see why anyone would choose to use EHMO if another method were available. Alan Shusterman, reed College, Portland, Oregon ==== #4 .....I wouln't want to use EHT to "explain" vibrational spectra, but it would and has been extremely useful in understanding molecular shapes. I will return to this point in a minute. problems that relate to angular variations are given quite well by EHT and this has been extensively documented in the literature Too much of what I see in the CCL postings relate to blind number crunching. If that is what one wants to do then I sincerely doubt that the EHM will be useful. But why should one do this? I strongly believe that a theoretician should either be predictive (and not in a derivative or trivial way) or offer theories about physical phenomena. Extended Hueckel performs admirably in the especially latter area. Thomas Albright, Professor and Graduate Chair, U of Houston ============== From elewars@alchemy.chem.utoronto.ca Sun Nov 16 18:54:09 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id SAA15730; Sun, 16 Nov 1997 18:17:38 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id SAA17177 for chemistry@www.ccl.net; Sun, 16 Nov 1997 18:17:36 -0500 (EST) Date: Sun, 16 Nov 1997 18:17:36 -0500 (EST) From: "E. Lewars" Message-Id: <199711162317.SAA17177@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: A PROGRAM TO ANIMATE GAUSSIAN FREQS: ANSWER 1997 Nov 16 Hello, This is in response to a question about a program that will animate Gaussian freq output. The Windows program MolWin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. FREQS: MolWin will also accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output: freq=(HPMode) MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. ==== NOTE: the inconveniently big Gaussian output can be made much smaller with an editor and still be read by MolWin; the essential parts are the Cartesian coordinates and the "long form" of the freqs, as shown in the example below. This speeds up MolWin's reading of the file (which also eats up maybe 20 times less space on your hard drive). E. Lewars ----- O=C=N-C=O radical, freqs, MP2/6-31G* G92 1997 Oct 29 Copyright (c) 1992, Gaussian, Inc. All Rights Reserved. ---------------------------------------------- # freq MP2/6-31G* scf=direct maxdisk=100000000 ---------------------------------------------- ------------------------------------------------- Radical (mult = 2) O=C-N-C=O; input: MP2 geom, Cs ------------------------------------------------- STOICHIOMETRY C2NO2(2) FRAMEWORK GROUP C1[X(C2NO2)] DEG. OF FREEDOM 9 FULL POINT GROUP C1 NOP 1 LARGEST ABELIAN SUBGROUP C1 NOP 1 LARGEST CONCISE ABELIAN SUBGROUP C1 NOP 1 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 -1.174440 -.367072 .000001 2 7 -.015605 .421966 .000000 3 6 1.164572 .050862 .000002 4 8 -2.304558 .011849 -.000001 5 8 2.325613 -.143912 -.000002 ---------------------------------------------------------- Rotational constants (GHZ): 112.9395192 2.4738711 2.4208440 Full mass-weighted force constant matrix: Low frequencies --- -13.6556 -.1619 -.0003 .0015 .0029 4.7354 Low frequencies --- 120.4172 170.4701 535.5204 0Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 4 5 ?A ?A ?A ?A ?A Frequencies --- 120.4057 170.4700 535.5204 591.8592 620.1372 Reduced masses --- 13.9540 14.5297 14.3216 12.6558 12.5723 Force constants --- .1192 .2488 2.4199 2.6120 2.8487 IR Intensities --- 2.3268 2.9694 5.9691 20.2035 14.1247 Raman Activities --- .0000 .0000 .0000 .0000 .0000 Depolarizations --- .0000 .0000 .0000 .0000 .0000 Coord Atom Element: 1 1 6 .00000 -.26971 -.30050 .00000 -.13003 2 1 6 .00000 -.14004 .44819 .00000 -.26110 3 1 6 .65818 .00000 .00000 .11988 .00000 1 2 7 .00000 .00026 .23642 .00000 -.07108 2 2 7 .00000 -.65058 .00889 .00000 -.28206 3 2 7 .36625 .00000 .00000 .31270 .00000 1 3 6 .00000 .09881 .31110 .00000 .18291 2 3 6 .00000 -.23159 .05483 .00000 .83428 3 3 6 .10397 .00000 .00000 -.87904 .00000 1 4 8 .00000 -.09710 -.57371 .00000 .00325 2 4 8 .00000 .40135 -.29511 .00000 .11300 3 4 8 -.55495 .00000 .00000 -.04104 .00000 1 5 8 .00000 .22509 .35877 .00000 .01930 2 5 8 .00000 .44702 -.09006 .00000 -.29610 3 5 8 -.33747 .00000 .00000 .33683 .00000 6 7 8 9 ?A ?A ?A ?A Frequencies --- 928.4373 1431.1212 1926.1061 2367.9502 Reduced masses --- 13.0098 14.4817 13.3669 12.7576 Force constants --- 6.6073 17.4752 29.2174 42.1469 IR Intensities --- 86.7287 88.0603 833.9814 744.9082 Raman Activities --- .0000 .0000 .0000 .0000 Depolarizations --- .0000 .0000 .0000 .0000 Coord Atom Element: 1 1 6 -.35954 .14062 -.76457 -.09516 2 1 6 -.66815 .19793 .24065 .06066 3 1 6 .00000 .00000 .00000 .00000 1 2 7 .00216 -.79373 .06901 -.32161 2 2 7 .52839 .01082 -.00153 .04951 3 2 7 .00000 .00000 .00000 .00000 1 3 6 .12483 -.06339 -.11284 .84912 2 3 6 -.12940 -.04048 .01577 -.15434 3 3 6 .00000 .00000 .00000 .00000 1 4 8 -.10391 .10564 .54936 .07336 2 4 8 .15569 -.02097 -.18872 -.02558 3 4 8 .00000 .00000 .00000 .00000 1 5 8 .27811 .53131 .04850 -.35744 2 5 8 -.01992 -.10663 -.00232 .05252 3 5 8 .00000 .00000 .00000 .00000 0Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 120.4057 170.4700 535.5204 THIS MOLECULE IS AN ASYMMETRIC TOP. ROTATIONAL SYMMETRY NUMBER 1. ROTATIONAL TEMPERATURES (KELVIN) 5.42021 .11873 .11618 ROTATIONAL CONSTANTS (GHZ) 112.93952 2.47387 2.42084 ZERO-POINT VIBRATIONAL ENERGY 51989.8 (JOULES/MOL) 12.42585 (KCAL/MOL) .0198018 (HARTREE/PARTICLE) 0Berny optimization. 0No z-matrix variables hence no action by Optmz. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad 1\1\UNIVERSITY OF TORONTO CHEMISTRY DEPARTMENT-ALCHEMY\FREQ\UMP2-FC\6-31G(D)\C2N 1O2(2)\ELEWARS\29-Oct-1997\0\\# FREQ MP2/6-31G* SCF=DIRECT MAXDISK=100000000\\Ra dical (mult = 2) O=C-N-C=O; input: MP2 geom, Cs\\0,2\C,0,-0.01192,-1.17592,-0.36 21\N,0,0.01389,-0.01389,0.4218\C,0,0.00152,1.16477,0.04611\O,0,0.0007,-2.30449,0 .0212\O,0,-0.00505,2.32501,-0.15327\\Version=HP-PARisc-HPUX-G92RevC.3\HF=-279.85 86329\MP2=-280.6037662\PUHF=-279.862544\PMP2-0=-280.6066228\S2=0.772\S2-1=0.76\S 2A=0.75\RMSD=5.145e-09\RMSF=1.253e-04\Dipole=-0.0045844,0.4907865,-0.1392956\Dip WHEN HAVING A MEETING OF THE MINDS, MAKE SURE YOU HAVE THE EQUIPMENT FOR IT. Job cpu time: 0 days 3 hours 56 minutes 41.5 seconds. File lengths (MBytes): RWF= 647 Int= 0 D2E= 0 Chk= 1 Scr= 0 0Normal termination of Gaussian 92.