From owner-chemistry@ccl.net Fri Nov 3 02:47:02 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id CAA19636; Fri, 3 Nov 1995 02:39:55 -0500 Received: from nic.bme.hu for MAILER-DAEMON@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id CAA21248; Fri, 3 Nov 1995 02:39:46 -0500 (EST) Received: from delfin.eik.bme.hu (delfin.eik.bme.hu [152.66.115.79]) by nic.bme.hu (8.6.12/8.6.12) with SMTP id IAA32038; Fri, 3 Nov 1995 08:39:08 +0100 From: csonka@web Received: from web (web.inc.bme.hu [152.66.63.16]) by delfin.eik.bme.hu (8.6.10/8.6.10) with SMTP id IAA26682; Fri, 3 Nov 1995 08:39:05 +0100 Received: by web (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA00959; Fri, 3 Nov 1995 10:38:40 +0100 Message-Id: <9511031038.ZM957@web.inc.bme.hu> Date: Fri, 3 Nov 1995 10:38:37 +0100 In-Reply-To: pitsel@chemul.uni.lodz.pl (Piotr Seliger) "CCL:G:summary AM1 vs PM3" (Nov 2, 8:19am) References: <9511020719.AA18481@chemul.uni.lodz.pl> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: pitsel@chemul.uni.lodz.pl (Piotr Seliger) Subject: Re: CCL:G:summary AM1 vs PM3 Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Pjotr, I was missing the original question and saw only the summary. I would like to draw your attantion to a very fundamental problem with the core repulsion function in PM3. It might have an unphysical minima which stabilize unrealistic H-H, C-H or O-H interactions. Some of the consequences were shown in the paper: J. Comp. Chem. 14 (1993) 895 by me and it was also reported in QCPE Bull. 11 (1991) 5. Be careful, because the QCPE figures contain errors. The reprints of J. Comp. Chem. 14 (1993) 895 are available in limited number >from me. Meantime I have discovered lot of unpublished problems which are related with this CRF problem. I have to say the problem is very serious. If you have structures with H-H distances below 2 angstrom it will occur. The AM1 is free from this error. Gabor -- Gabor I. Csonka Budapest University of Technology FAX: (361) 463.36.42 Inorganic Chemistry Dept. Ch. Bldg csonka@web.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 http://www.fsz.bme.hu/bme/chemical/csonka.html From VARNAI@ch.bme.hu Fri Nov 3 09:47:07 1995 Received: from ns.bme.hu for VARNAI@ch.bme.hu by www.ccl.net (8.6.10/950822.1) id JAA25081; Fri, 3 Nov 1995 09:35:08 -0500 Received: from ch.bme.hu (ch.bme.hu [152.66.64.1]) by ns.bme.hu (8.6.12/8.6.12) with SMTP id PAA31263 for ; Fri, 3 Nov 1995 15:34:02 +0100 Received: from CH/TEMPQ by ch.bme.hu (Mercury 1.12); Fri, 3 Nov 95 15:50:39 +1100 Received: from TEMPQ by CH (Mercury 1.12); Fri, 3 Nov 95 15:50:25 +1100 From: "Varnai Peter" To: chemistry@www.ccl.net Date: Fri, 3 Nov 1995 15:50:17 GMT+100 Subject: CASSCF questions X-Confirm-Reading-To: "Varnai Peter" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <6EEC8956B7E@ch.bme.hu> Dear CClers, I would need Your help to understand the practical tricks in CASSCF calculations. 1, One needs to define an active space. -At this point quantum chemists start to think as the conventional organic chemist,in localized orbitals. Here those orbitals needed -in view of a chemist- that are involved in a eg. reaction (forming/breaking orbitals). -A more exact answer would be that those orbitals needed which are important in "excitation" to give configurations that contribute to the total energy significantly. So: -according to the first approach one would visualize the MOs. Here he/she would realize that in MO theory the orbitals are spread all over the molecule, so the needed eg C-C bond will appear in at least 3 MOs. Which one should be used then? Let's use all (unfortunately, the valence MOs usually can't be all involved in the active space)? Let's localize the MOs with standard methods? Pick one random and what happens (the one is better than the other if using it the SCF energy is lower)? -according to the more "mathematical" approach let's calculate a CISD wavefunction [in the absence of the full CI :(] and involve the orbitals which are involved in large coefficient (say 0.03<) determinants? And what if the HF reference function was not a good approximation and some important determinants are missed? -If I am right CAS should be used as the correction to the non- dynamic electron correlation (through the the right geometry and wavefunction). What happens then when CISD tells you that an orbital energetically important though not needed in view of the reaction, description of the radical etc. it would be some parts of the dynamic correlation effect then?! 2, CASSCF in Gaussian 92 for me (and I guess for several others) stopped with the error message: rotation larger than 45 degree... If I understand well either a smaller step in wavefunction optimization would have been desirable or the active space was not well chosen and a non-selected orbital was crucial in the active space. Yet, I haven't got error message like this with the G94 routine, only warnings that large rotations are scaled and something like: I J= 12 26. I don't really understand the meaning of these numbers (i,if these are MO numberings, I have to say that eg MO- 12 was not selected to be in the active space, ii, in MOLCAS for example the user can define only the number and symmetry of the active orbitals, the exact MO not, how will then the routine pick the right orbital? iii, is it allowed to change orbitals of the active space during SCF). 3, In case one loses the chk file and would like to keep it for further use, is the following way is correct to create the same chk file? 1, Calculate the HF-MOs at the starting geometry once again and picking the same MOs 2, converging the CAS wavefunction as it was done in the previous calculation and 3, reading in the wavefunction (to have the same active space) and having the converged CAS-geometry (not to redo the whole previous calculation). If it is correct can anyone tell me why I did not reproduce the same stationary point, but locating an other one (higher in energy). (As I know this method is used when one tries to find the right active space in a supermolecule by isolating it to fragments). If You had the patience and read my letter through, and You can help me in using CAS smoothly: THANK YOU! Varnai Peter PhD student varnai@ch.bme.hu From olsonl@darwin.pprd.abbott.com Fri Nov 3 10:32:08 1995 Received: from abtlabs.pprd.abbott.com for olsonl@darwin.pprd.abbott.com by www.ccl.net (8.6.10/950822.1) id KAA26030; Fri, 3 Nov 1995 10:21:30 -0500 Received: from darwin.pprd.abbott.com by abtlabs.pprd.abbott.com with SMTP id AA24000 (5.65c/IDA-1.4.4 for ); Fri, 3 Nov 1995 09:21:26 -0600 Received: by darwin.pprd.abbott.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id JAA21196; Fri, 3 Nov 1995 09:24:25 -0600 Date: Fri, 3 Nov 1995 09:24:25 -0600 From: olsonl@darwin.pprd.abbott.com (Leif P. Olson) Message-Id: <199511031524.JAA21196@darwin.pprd.abbott.com> To: CHEMISTRY@www.ccl.net Subject: Proton barrier heights in PM3 A referee for a paper I submitted states that "PM3 is well-known to overestimate proton barrier heights". He/she may be right (although this has no effect on the conclusions in the paper), but in any case I need to find a specific reference which addresses this "well-known" fact. I would appreciate it if someone could point me to such a reference. Thank you. Leif Olson, Ph.D. olsonl@darwin.pprd.abbott.com Department of Structural Biology Abbott Laboratories Abbott Park, IL From jstewart@fujitsuI.fujitsu.com Fri Nov 3 11:17:08 1995 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.10/950822.1) id LAA27738; Fri, 3 Nov 1995 11:05:14 -0500 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [133.164.254.1]) by mail.barrnet.net (8.7.1/MAIL-RELAY-LEN) with SMTP id IAA19895 for ; Fri, 3 Nov 1995 08:05:14 -0800 (PST) Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA11352; Fri, 3 Nov 95 08:06:49 PST Date: Fri, 3 Nov 95 08:06:49 PST From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9511031606.AA11352@fujitsu1.fujitsu.com> To: CHEMISTRY@www.ccl.net Subject: MOPAC 93: bug report may be premature Bug in MOPAC 93 ? Yesterday I reported what might be a bug in the calculation of the transition dipole in MOPAC 93. This report resulted in several people telling me that the ground-state dipole is , and that obviously can be non-zero. The potential bug was reported because users have a right to believe that the software they are running does in fact work correctly. Perhaps I `jumped the gun' in announcing a bug without doing more homework. Now for an update. All tests on the transition dipole have failed to show that a bug does in fact exist. However, and here is where I need help, there is a point of theory that I don't understand. That is, for a transition dipole, which of the two following statements is true: 1: = + 2: = - where psi is an atomic orbital, a molecular orbital, a microstate, or a state function. Yes, I know this looks trivial, but for just now it's got me confused. MOPAC 93 uses statement 1. In the meantime, the available evidence is that the transition moment calculation is correct, within the approximations used. If statement 2 is correct, then the transition dipoles will be in error by a few percent. Any comments on this would be appreciated. James J. P. Stewart From owner-chemistry@ccl.net Fri Nov 3 13:02:09 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA01052; Fri, 3 Nov 1995 12:58:37 -0500 Received: from ubvmsb.cc.buffalo.edu for CHE9985@ubvms.cc.buffalo.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA25556; Fri, 3 Nov 1995 12:58:35 -0500 (EST) Received: from ubvms.cc.buffalo.edu by ubvms.cc.buffalo.edu (PMDF V4.3-9 #5889) id <01HX7GVA3STC8WWGUA@ubvms.cc.buffalo.edu>; Fri, 03 Nov 1995 12:56:15 -0500 (EST) Date: Fri, 03 Nov 1995 12:56:15 -0500 (EST) From: "Dr. Zhengwei Su" Subject: Summary --- Polarization functions for transition metals To: chemistry@ccl.net Message-id: <01HX7GVA6E1U8WWGUA@ubvms.cc.buffalo.edu> Organization: University at Buffalo X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: CHE9985 MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Summary --- Polarization functions for transition metals My sincere thanks to the following for their replies: J. Lohrenz (lohrenz@oci.unizh.ch) S. Dapprich (dapprich@Mailer.Uni-Marburg.DE) A. Ehlers (ehlers@iodine.chem.vu.nl) P.-O. Norrby (peon@medchem.dfh.dk) All point to the following paper: A. W. Ehlers, M. Boehme, S. Dapprich, A. Gobbi, A. Hoellwarth, V. Jonas, K. F. Koehler, R. Stegmann, A. Veldkamp and G. Frenking, Chem. Phys. Lett. 1993, 208, 111. The values for Fe, Co, Ni are 2.462, 2.780 and 3.130 resp. The reply from Dr. P.-O. Norrby has additional information and his message is included here in its entirety: There are, but of course only for use with specific basis sets. Frenking et al. have optimized the simplest possible type of f-functions (just 1 gaussian) for use with one of Hay & Wadt's ECP:s, I believe you could use them with, for example, LANL2DZ. The reference is "Ehlers et al., Chem.Phys.Lett. 208 (1993) 111", the single gaussian exponents for Fe, Co, and Ni are 2.462, 2.780, and 3.130, respectively. I have, by personal communication, got more extensive polarizations for other TM's, you could try to make a literature search for Margareta Blomberg and Per Siegbahn, that should give you some pointers. > My original question: > > Dear CCLers: > Are there optimized parameters for f-type polarization functions > for first-row transition metals such as Fe, Co and Ni? Any pointers > will be appreciated. > > Z. Su > SUNY at Buffalo > From owner-chemistry@ccl.net Fri Nov 3 13:47:11 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA01882; Fri, 3 Nov 1995 13:40:09 -0500 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by bedrock.ccl.net (8.7.1/950822.1) id NAA25803; Fri, 3 Nov 1995 13:40:03 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA07975; Fri, 3 Nov 95 10:39:54 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma007972; Fri Nov 3 10:39:27 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA18403; Fri, 3 Nov 95 10:39:20 -0800 From: "Wayne Huang" Message-Id: <9511031039.ZM18401@mazda.wavefun.com> Date: Fri, 3 Nov 1995 10:39:19 -0800 In-Reply-To: csonka@web "CCL:summary AM1 vs PM3" (Nov 3, 10:38am) References: <9511020719.AA18481@chemul.uni.lodz.pl> <9511031038.ZM957@web.inc.bme.hu> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: csonka@web.inc.bme.hu, olsonl@darwin.pprd.abbott.com Subject: Re: CCL:summary AM1 vs PM3 Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 To echo Gabor Csonka's comments on PM3's problem of unrealistic estimation of H-H interaction, here are some additional comments on the problem and fix-up solution. Original PM3 Bug: ---------------- In original PM3 model, the non-hydrogen interaction are known to be problematic which is too attractive and gives rise to unusual stability for crowded arrangements. PM3 Expt === === methyl cyclohexane: (axial) <-> (equatorial) 1.1 1.8 t-butyl cyclohexane: (axial) <-> (equatorial) 1.1 5.4 Modification: ------------ This can be corrected by introducing a repulsive term between non-bonded hydrogens into the PM3 energy expression, which allows it rapidly approaches to zero with increasing H--H distance and becomes insignificant for distances greater than about 2 angstrom. PM3 PM3 Expt (modified) === === === methyl cyclohexane: (axial) <-> (equatorial) 1.1 1.3 1.8 t-butyl cyclohexane: (axial) <-> (equatorial) 1.1 4.8 5.4 This result is little if any change for systems which are not crowded, but significant change for molecules in which hydorgens are crowded t together. This modification is within Spartan semiempirical module. The correction has been introduced as the default for PM3(tm) (the PM3 method dealing with d-transition metals) and as an option for PM3. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From te_meehan@ccmail.pnl.gov Fri Nov 3 14:32:11 1995 Received: from pnl.gov for te_meehan@ccmail.pnl.gov by www.ccl.net (8.6.10/950822.1) id OAA02970; Fri, 3 Nov 1995 14:28:08 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HX7DY0TMQO8WVYK4@pnl.gov>; Fri, 03 Nov 1995 11:27:56 -0800 (PST) Date: Fri, 03 Nov 1995 11:25 -0800 (PST) Subject: TS refinement To: chemistry@www.ccl.net Message-id: <01HX7DY0VA368WVYK4@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT To the lot: Here are two very helpful responses regarding refinement of TS structures in MOPAC; so that the IRC will work properly. tim meehan --------------------- The "gradients too large" _I think_ probably arises because somewhere along the line of the IRC calculation, there is a FORCE calculation. FORCE expects to see the the GNORM<5.0. You can _probably_ overrride this with a LET keyword. . .But I wouldn't advise this. Try an EF to refine the structure (I guess you should use TS since this is t he transiition state), specifying a GNORM on the order of 2 or so. Do a FORCE to be sure you are still at the TS (one -ve root to the Hessian), before trying the IRC=+/-1 stuff. If your are still in the ballpark, you should be able to reduce the gradient even further. . .this is physically "real" since the residual forces on the atoms will influence the IRC. . .or so it seems to have happened to me! >From Painful experience, there are not shortcuts. If you have more than one -ve frequency, use the prcedure Stewart outlines to "escape from a hilltop". Hope this is helpful, sb ----------------------- I've recently found that a useful trick for refinement of stubborn transition states is to take the best that you have & use the SIGMA keyword in *AMPAC* [MOPAC hasn't got it]. It sometimes works when nothing else will. A word of warning: I've found instances of when AM1 **seems** to be closing in on a ts, but there's NO WAY to refine it-- if I tried, the molecule fell apart. When I ran the corresponding reaction coordinate with ab initio me- thods, I found the reaction to be monotonically decreasing in energy toward fragmentation. Of course, I don't know what you've tried, or what your ridiculous TS's look like, but I hope these experiences may be of some use. Good luck! Irene Newhouse