From FRENKING@DMRHRZ11.bitnet Thu Oct 29 01:35:36 1992 Date: Thu, 29 Oct 92 07:35:14 CET To: chemistry-request@ccl.net From: FRENKING%DMRHRZ11.BITNET@vm.gmd.de Hallo, could you please forward the following message, which is an answer to a question posted to the list, to the general net? We have trouble getting a subject entry, we are working on it. Thank you, Gernot Frenking > From chemistry-request@ccl.net Wed Oct 21 16:33:19 1992 > To: CHEMISTRY@oscsunb.ccl.net > Subject: Transition Metal Calculations > Sender: chemistry-request@ccl.net > > Hi, > Having recently joined this list I would like to ask about available > programs that perform geometry optimisation on systems including > 2nd row transition metals. I realise an ab initio packake would > handle this but the systems are large and would require too > much cpu time. I suppose I'm looking at semi-empirical programs ? > > Thanks for any help. > > john upham > > John Upham, School of Chemistry, University of Reading, Berks., RG6 2AD, UK. > Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet)Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator > OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net > --- > > We recently published a systematic test of the accuracy of ECP methods for geometries of transition metal compounds using various contraction schemes and different ECPs (J. Comput. Chem. 13 (1992) 919). Although this paper deals only with Ti compounds, we studied many other TM compounds, in particular Cr, Mo, W, Fe, Os compounds. The conclusions drawn in that paper are the same for other TM molecules. Actually, the results for 2nd and 3rd row TM compounds are even better than for first row TMs. Relativistic contributions are included for 2nd and 3rd row TMs, but I don't thin that this is the reason for the better results. You should use ECPs which include the (n-1)s and (n-1)p electrons in the valence space, i.e. the (n)s and (n-1)d valence space is too small. If you use the Gaussian programs, you have to type the parameters for the corresponding Hay/Wadt ECPs. Unfortunately, Gaussian has only the small valence ECP of Hay and Wadt as standard basis sets, called LANL1MB and LANL1DZ. DON'T USE THEM FOR TM COMPOUNDS!! Geometries of TM compounds in high oxidation states are calculated with good accuracy at the HF level. For molecules in low oxidation states, e.g. for carbonyl complexes, you have to include correlation energy such as MP2. This can become expansive. DF methods are an alternative. Semiempirical methods suffer from the fact that there are not many experimental data to optimize parameters. ++++++++++++++++++++++++++++++++++++++++ Gernot Frenking, Prof. FB Chemie, Universitaet Marburg Hans-Meerwein-Strasse D-3550 Marburg Germany Tel.(06421)285563 frenking@dmrhrz11.bitnet ++++++++++++++++++++++++++++++++++++++++ From m10!frisch@uunet.UU.NET Thu Oct 29 06:00:56 1992 Date: Thu, 29 Oct 92 11:00:56 EST From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: ECP's for ab initio for metals To: chemistry@ccl.net Gernot Frenking noted some useful results of his indicating the importance of including the (n-1)s and (n-1)p electrons in TM calculations. In their original work, Hay and Wadt found that these next lower shells vary in importance depending on where in the transition series an atom lies. I would agree, however, that the smaller expansions should be used only after very carefuly scrutiny. In any case, contrary to what Gernot said, Gaussian 92 DOES have both flavors of Los Alamos potentials and basis sets. Use LANL1MB and LANL1DZ for the smaller expansion, or LANL2MB and LANL2DZ to include the (n-1)s and (n-1)p electrons and basis functions. Mike Frisch ------- From theresa@si.fi.ameslab.gov Thu Oct 29 04:53:07 1992 From: theresa@si.fi.ameslab.gov (Theresa Windus) Subject: TM calculations To: chemistry@ccl.net () Date: Thu, 29 Oct 92 10:53:07 CST Concerning John Upham's message about TM calculations: The computational package GAMESS has many ECPs for TM calculations. You might want to consider using it. GAMESS is a free program (under the restriction that you do not distribute it) and is available by sending an e-mail message to Michael Schmidt at mike@si.fi.ameslab.gov Good luck!! Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 USA e-mail: theresa@si.fi.ameslab.gov From WERPETIN%XASW@ecs.umass.edu Mon Oct 29 08:24:10 1992 Date: 29 Oct 1992 13:24:10 -0500 From: Katrina Werpetinski Subject: Xalpha LDF gradients To: chemistry@ccl.net I've got another problem with which I'm hoping someone can help. We're using an Xalpha LDF code to do geometry optimizations. The gradient calculations wrt Cartesian coordinates are not conserving linear and angular momentum; that is, there are net translational and rotational energies. This, of course, makes it impossible to find gradients wrt internal coordinates. Has anyone come up against this problem before and fixed it? I believe we've got the correct implimentation for calculating the gradients by following, for example: J.W. Mintmire, IJQCS, 24 (1990), 851-857 B.I. Dunlap and N. Rosch, J Chim Phys, 86 (1989), 671-688 B.I. Dunlap, J. Andzelm, J.W. Mintmire, Phys Rev, 42 (1990),6354-6359 Thank you, Katrina werpetin@ecs.umass.edu =-=-=-= The following is a sample of what I'm talking about. Hydrogen Peroxide Input: o1 o2 1 ROO h1 1 ROH 2 AOOH h2 2 ROH 1 AOOH 3 AHOOH ROO = 2.7 ROH = 1.8 AOOH = 100.0 AHOOH = 100.0 Cartesian coordinates: Site Atomic # Coordinates (au) 1 O1 8 0.000000 1.350000 -0.126604 2 O2 8 0.000000 -1.350000 -0.126604 3 H1 1 1.357932 1.662567 1.012836 4 H2 1 -1.357932 -1.662567 1.012836 Gradients: Site dE/dx dE/dy dE/dz 1 O1 0.121405325 -0.014464327 0.065483102 2 O2 -0.121405325 0.014464327 0.065483102 3 H1 -0.116163851 -0.041976312 -0.095041532 4 H2 0.116163851 0.041976312 -0.095041532 From urquhart@mcmail.cis.mcmaster.ca Thu Oct 29 09:19:20 1992 Date: Thu, 29 Oct 1992 14:19:20 -0500 (EST) From: Stephen Urquhart Subject: Re: d orbitals in semiempirical calculations. To: Dr D Buttar On Wed, 28 Oct 1992, Dr D Buttar wrote: > I would like to perform some semiempirical calculations on > chlorine containing compounds, but want to include d orbitals. > Could anyone inform me which semiempirical programs allow the > inclusion of parameters for d orbitals. > > Many Thanks, > David Buttar > University of Warwick > Extended Huckel (EHMO) allows you to include 3d orbitals for chlorine. QCPE has the code, but there a site you can ftp it from, if you are interested. Cheers, Stephen Urquhart From friedman@tammy.harvard.edu Thu Oct 29 11:15:55 1992 Date: Thu, 29 Oct 92 16:15:55 -0500 From: friedman@tammy.harvard.edu (Dawn Friedman) To: chemistry@ccl.net Subject: G92 psi symmetry Dear netters, On page 150 of the g92 manual, users who require a particular set of orbital symmetries for a wavefunction, and who have specified guess=alter and gotten a correct starting set of orbitals, but who find that the final wavefunction has reverted to the unwanted orbital symmetries, are advised to use SCF=QC or SCF=DM, "which usually holds symmetry from one iteration to the next." Well, this time neither option held symmetry. Does anyone know of a surer option? Many thanks, Dawn From st-amant@cgl.ucsf.EDU Thu Oct 29 05:52:29 1992 Date: Thu, 29 Oct 92 13:52:29 -0800 From: st-amant@cgl.ucsf.edu (Alain St-Amant) To: WERPETIN%XASW@ecs.umass.edu, chemistry@ccl.net Subject: Re: Xalpha LDF gradients werpetin@ecs.umass.edu writes: > I've got another problem with which I'm hoping someone can help. We're > using an Xalpha LDF code to do geometry optimizations. The gradient > calculations wrt Cartesian coordinates are not conserving linear and > angular momentum; that is, there are net translational and rotational > energies. This, of course, makes it impossible to find gradients wrt > internal coordinates. Has anyone come up against this problem before > and fixed it? I ran into the same problem when I implemented gradients into my DFT software. Though the gradient is analytical, approximations have to be made, and an error due to the incompleteness of the exchange-correlation basis set brings about the loss of translational and rotational invariance (as well as slight errors, about 0.005 Angstroms in bond lengths and 0.5 degress in bond angles). I got around the translational and rotational invariance problem by calculating the net translation of the center of the molecule (center of mass if all atoms were assigned the same mass) and the net angular momentum and then adding forces "equal but in the opposite direction" that eliminate the net translation and rotation. it seems to work. without this trick, I could not geometry optimize either. If anybody has a more rigorous method, I'd like to hear about it also. Hope this helps, alain st-amant department of pharmaceutical chemistry, university of california, san francisco From B_DUKE@DARWIN.NTU.EDU.AU Fri Oct 30 08:46:36 1992 Date: Fri, 30 Oct 1992 8:46:36 GMT From: B_DUKE@DARWIN.NTU.EDU.AU (Brian Duke) Subject: ECPs and the GAUSSIAN LAN* basis sets. To: CHEMISTRY@ccl.net Mike Frisch has given us some most useful information about the LAN basis sets. I have two other questions that people on the list may be able to answer:- What is the best way to add polarisation d functions to the LAN* basis sets? Is this necessary and under what circumstances? Thanks (and Jan - keep up the good work. We appreciate it "Down under") Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University GPO Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 FAX 089-410460 E-mail B_DUKE@DARWIN.NTU.EDU.AU From CUNDARIT@MEMSTVX1.bitnet Thu Oct 29 12:34:00 1992 Date: Thu, 29 Oct 92 17:34 CDT From: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: More TM calcs. To: chemistry@ccl.net Concerning TM calcs, I'd like to follow up on Thersa Windus' comments on transition metal calcs. We've probably used GAMESS (Iowa State version) as extensively for transition metals as anyone else and from our point of view the big benefit to GAMESS is the built-in ECPs from Walt Stevens and co., the so-called SBKJs (Can. J. Chem. 1992, 70, 612). We have had quite good success in predicting geometries, rotational barriers, reaction barriers and the like using the SBKJs, which are formally triple-zeta for the "valence" nd, (n+1)s and (n+1)p. They also include the (n-1)s and (n-1)p outer core which the concensus seems to indicate are essential. To my knowledge, the SBKJ for the s- and p-block elements are built in Gaussian, but not for the d-block although they can be entered manually. Now that the SBKJs have been published I encourage anyone interested in getting into TM-containing systems to give them a whirl in their favorite program. Folks have, of course, have taken the basic Hay-Wadt scheme and augmented the basis sets and done some excellent TM work; the research of Morokuma, Hall and their collaborators come to my mind, but undoubtedly there are others. The work of Gernot Frenking is the first methodical analysis that I have seen of the various core size and basis set augmentation schemes for the Hay-Wadt. I highly recommend Gernot's article to anyone planning on getting into TM calcs. There are also the ECP schemes of Ross, Ermler, Pitzer, et al.; if my understanding is correct, this group has now extended their scheme to the entire Periodic Table! Doesn't CADPAC include Huzinaga's model potentials for the d-block? Preuss and company have published ECP schemes for the lanthanides, and we have extended the SBKJ scheme to the lanthanides. Thus, the ECP options in ab-initio calcs. are rapidly growing, definitely worth a look for anyone interested in the nether regions of the Periodic Table. Tom Cundari Assistant Professor Department of Chemistry Memphis State University Memphis, TN 38152 From marcus@acsu.buffalo.edu Thu Oct 29 17:27:42 1992 From: marcus@acsu.buffalo.edu (Emil Marcus) Subject: Proteins Structure. Coordinate Conversion: Internal --> Cartesian (PDB) To: chemistry@ccl.net Date: Thu, 29 Oct 92 22:27:42 EST I would be most grateful if you could help me locate a program that converts protein internal (dihedral angles: phi, psi, omega, chi's...)coordinate files into cartesian - PDB (Protein Data Bank) type files ! The program that does the reverse transformation is available from The Protein Data Bank... Thank you, Emil -- *** marcus@acsu.buffalo.edu ***