From chemistry-request@server.ccl.net Sun Jan 2 15:25:00 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30106 for ; Sun, 2 Jan 2000 15:25:00 -0500 Received: from bedrock.ccl.net (bedrock.ccl.net [192.148.249.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id OAA06565; Sun, 2 Jan 2000 14:16:44 -0500 (EST) Date: Sun, 2 Jan 2000 14:16:46 -0500 (EST) From: Jan Labanowski To: "Carlos Robles V. " cc: Jan Labanowski , chemistry@ccl.net Subject: Re:internal/xyz coordinates In-Reply-To: <200001021624.NAA03807@mail1.manquehue.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT Dear Carlos, N atoms in space have 3N cartesian coordinates. But some of this information is redundant, since they also provide the orientation, which does not change the relations between atams. Assuming that atoms of your molecule do not lie on the straight line, you can rotate the molecule around 3 orthogonal (i.e., perpendicular axes) and move it independently in three dimension without changing any relation between atoms. So, in fact, there is 3N-6 values which are needed to specify relation between atoms. You only have bond lengths between atoms, i.e., N*(N-1)/2 values, which is only enough to specify uniquely the relation in the molecule with 2 atoms. For larger moleculues you need more data (angles or additional distances). You may want to read more about this in: http://www.ccl.net/cca/documents/molecular-modeling/ Jan Labanowski jkl@ccl.net On Sun, 2 Jan 2000, Carlos Robles V. wrote: > Hi everybody; > > I wish you a very happy year 2000, and of course for the rest of the > century. I have a problem, and I hope someone can help me.. > > I need to know the real xyz coordinates (coordinates in space) of simple > organic > molecular structures. But the problem is that I only know the atoms and the > bonds between them. > > How can I do ? > I would like have every coordinates in zero (x=y=z=0) and to pass the input > file to a program or function that translate the information to real (or > almost) xyz coordinates. > Do you know a program like that ? > I´ve tryed with Tinker, but this program requieres certain that input file > is in format .PDB, and that format I can't to obtain directly from your > output file. > > The global question is : Can I translate my file in another that > contains the real (or almost) orthogonal coordinates ? > > Note : > - I work under Linux. > - My file is something like this (a very simple structure): > > atoms > C1 > C2 > H1 > H2 > H3 > H4 > H5 > H6 > bonds > C1 H1 > C1 C2 > C1 H2 > C1 H3 > C2 H4 > C2 H5 > C2 H6 > > Greetings, Carlos Robles . > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Mon Jan 3 01:20:43 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA32658 for ; Mon, 3 Jan 2000 01:20:42 -0500 Received: from bedrock.ccl.net (bedrock.ccl.net [192.148.249.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id AAA10817; Mon, 3 Jan 2000 00:12:19 -0500 (EST) Date: Mon, 3 Jan 2000 00:12:21 -0500 (EST) From: Jan Labanowski To: "Carlos Robles V. " cc: chemistry@ccl.net Subject: More on internal/xyz coordinates In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Actually I was wrong here... (It was a long night {:-)}...). I glanced at it again, and found major problem... You do not have N*(N-1)/2 distances... You have only bonds. And this is not related to the number of atoms, but to sum of valences if individual atoms. Beside the simplest molecules, like diatomics, cyclic triatomics, or highly symmetric systems, the bond lengths are not enough to specify the internal geometry of molecules, and you will need angles or distances between nonbonded atoms. In fact, for molecules with more than 4 atoms, providing all interatomic distances will be more than enough (system will be overdetermined), since these distances are dependent on each other... E.g.,: No. of atoms No. of possible distances No. of degress of freedom N N*(N-1)/2 3N-6 (for nonlinear) 1 0 0 2 1 1 (3N-5 linear) 3 3 3 4 6 6 5 10 9 6 15 12 On Sun, 2 Jan 2000, Jan Labanowski wrote: > Dear Carlos, > > You only have bond lengths between atoms, i.e., > N*(N-1)/2 values, which is only enough to specify uniquely the relation > in the molecule with 2 atoms. For larger moleculues you need more data > > http://www.ccl.net/cca/documents/molecular-modeling/ Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Mon Jan 3 05:40:51 2000 Received: from techunix.technion.ac.il (mailer@techunix.technion.ac.il [132.68.1.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA01209 for ; Mon, 3 Jan 2000 05:40:49 -0500 Received: from tx.technion.ac.il (unknown [132.68.86.138]) by techunix.technion.ac.il (Postfix) with ESMTP id CC2DC870F for ; Mon, 3 Jan 2000 11:32:35 +0200 (IST) Sender: irena@techunix.technion.ac.il Message-ID: <3870CF89.1788031B@tx.technion.ac.il> Date: Mon, 03 Jan 2000 16:34:17 +0000 From: Irena Efremenko X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.7 i686) X-Accept-Language: en, ru MIME-Version: 1.0 To: CHEMISTRY@server.ccl.net Subject: NBO - Population inversion Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit HELLO, Some time ago there was a discussion on Population inversion in NBO. I would like to know your opinion on 1. "Physical" meaning of this inversion in terms of localized orbitals. More generally, how can I understand that "one of 3d orbital lies below in energy, but it's population (occupancy) is lower than 4s or any of 4p orbitals"? Does it means this 3d AO contributes to higher MO? 2. The main purpose of NBO analysis was to overcome "unphysical" (negative) populations. NBO often provides different orbital populations and even different charges for symmetric atoms. Is it "physical" picture? 3. In spite of the similar mathematics DFT has nothing to do with atomic or molecular orbitals. Thus, any population analysis on DFT density is "computational" mixing of two different approaches. True or wrong? Thanks in advance, -- Dr. Irena Efremenko Wolfson Department of Chemical Engineering Technion - Israel Institute of Technology Haifa 32000, Israel Phone: 972-4-8293561 Fax: 972-4-8230476 > Those WARNINGs are quiet usual. When NBO program prints > Natural Atomic Orbitals (1s, 2s, 3s etc. ), it does on the basis of > the energy order or on the basis of occupancy. The WARNING message > "Population inversion" comes when, the orbital occupancies and energy ordering > don't match or don't coincide. suppose, for example when one of 3d orbital lies > below in energy, but it's population (occupancy) is lower than 4s or any of 4p > orbitals, then population inversion occurs and should print warning massage. > > For core (NAO treated as unhybridized single center core NBO) orbitals, which in > > formal Lewis sense should be filled by 2 electrons. Sometimes due to unphysical > mixing > of core and valence lone pairs, the core occupancy goes below the threshold > <1.9990e) and > should print worning massage > > However, your NBO analysis should be ok. > > Cheers. > > Jamal > > ------------------------------------------------------- > Md. Jamal Uddin > AK Frenking > Fachbereich Chemie > Philipps-Universität Marburg > D-35032, Marburg > Germany > > email: jamal@chemie.uni-marburg.de > Tel : +49 6421 285549 > -------------------------------------------------------- > > Maija Lahtela wrote: > > > Dear CCLers, > > > > I am trying to do NBO (Natural Bond Orbital) analysis within > > Gaussian98 ( options for calculation b3lyp/6-311+g* scf=tight pop=nboread > > IOP(3/59=9)). In the middle of calculations following warning appear: > > > > WARNING: 1 low occupancy (<1.9990e) core orbital found on P 3 > > 1 low occupancy (<1.9990e) core orbital found on C 5 > > > > WARNING: Population inversion found on atom P 3 > > Population inversion found on atom O 4 > > Population inversion found on atom C 5 > > Population inversion found on atom C 6 > > Population inversion found on atom C 7 > > Population inversion found on atom C 8 > > Population inversion found on atom C 9 > > Population inversion found on atom C10 > > Population inversion found on atom O11 > > Population inversion found on atom S13 > > > > I am not sure I understand what happend. Can somebody > > give me some hints or comments on that? > > Thank you for your help in advance > > > > Sincerely Yours, > > Maija Lahtela-Kakkonen > > > > *************************************** > > Maija Lahtela-Kakkonen > > Researcher > > CSC-Center for Scientific Computing > > P.O.Box 405 > > FIN-02101 ESPOO FINLAND > > TEL 358-9-4572079 > > FAX 358-9-4572302 > > E-MAIL mlahtela@csc.fi > > *************************************** From chemistry-request@server.ccl.net Mon Jan 3 09:44:47 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03283 for ; Mon, 3 Jan 2000 09:44:47 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id OAA15491 for ; Mon, 3 Jan 2000 14:36:32 +0100 (MET) Date: Mon, 3 Jan 2000 14:36:32 +0100 (MET) Message-Id: <200001031336.OAA15491@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Convergence problem Hi all, let's start with the best wishes for all of you in the next year ! I've been trying a TD-DFT calculation (SP) with Gaussian98 and I've got the following message: << Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -543.828916188 A.U. after 65 cycles Convg = 0.3546D+01 -V/T = 2.0021 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/bin/g98.a7/l502.exe >> What keyword is best used to be able to solve this problem ? Maxcycle ? Perhaps it's a problem with the grid ? All suggestions are welcome. I'll summarize. Thanks Serge Kwasniewski _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Mon Jan 3 12:09:48 2000 Received: from ap.stmarys.ca (ap.StMarys.CA [140.184.21.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA03895 for ; Mon, 3 Jan 2000 12:09:47 -0500 Received: from localhost (cpye@localhost) by ap.stmarys.ca (8.8.8/8.8.8) with ESMTP id MAA09458 for ; Mon, 3 Jan 2000 12:01:28 -0400 (AST) Date: Mon, 3 Jan 2000 12:01:28 -0400 (AST) From: Cory Pye X-Sender: cpye@ap To: chemistry@ccl.net Subject: The first ever ab initio calculation OR y2k noncompliance in G92. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody, I thought that the readers of the CCL would appreciate a bit of chemistry y2k humour. The following is the output of a calculation that I just ran using Gaussian 92. Please note the date on the first line. 1\1\GINC-TEMPUS.UCS.MUN.CA\FOPT\RMP2-FC\Gen\H2O5S1(2-)\CORY\3-Jan-1900 \1\\#N MP2 CHKBAS OPT=READFC GEOM=CHECK GUESS=READ SCF=DIRECT MAXDISK= 75000000\\SO4_2-_Aq1_C2v\\-2,1\S\X,1,1.\O,1,O1S,2,O1SD\O,1,O1S,2,O1SD, Enjoy! -Cory ************* ***************** ! Dr. Cory C. Pye *** ** ** ** ! Assistant Professor ** * **** ! Theoretical and Computational Chemistry ** * * ! cpye@crux.stmarys.ca ** * * ! http://www.cobalt.chem.ucalgary.ca/cory *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) From chemistry-request@server.ccl.net Mon Jan 3 12:26:39 2000 Received: from aragorn.ics.muni.cz (aragorn.ics.muni.cz [147.251.4.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04053 for ; Mon, 3 Jan 2000 12:26:37 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by aragorn.ics.muni.cz (8.8.5/8.8.5) with ESMTP id RAA01977 for ; Mon, 3 Jan 2000 17:18:18 +0100 (MET) Received: (from czernek@localhost) by bilbo.chemi.muni.cz (8.8.5/8.8.5) id RAA24049; Mon, 3 Jan 2000 17:19:49 +0100 (MET) From: Jiri Czernek Message-Id: <200001031619.RAA24049@bilbo.chemi.muni.cz> Subject: Summary: NMR tensors in GAUSSIAN To: chemistry@ccl.net Date: Mon, 3 Jan 100 17:19:49 +0100 (MET) Cc: czernek@bilbo.chemi.muni.cz (Jiri Czernek) X-Mailer: ELM [version 2.4ME+ PL32 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL-ers , At the end of the last year I asked > how to obtain eigenvalues and -vectors of MP2 tensors > in g98 as simply as possible. Can somebody help before Y2K? :-) I'll summarize > the answers, of course. and really got THE answer before Y2K. Instead of a summary I'd like just to inform you that when using Rev A.7 of GAUSSIAN98, run your calculation with NMR=PRINTEIGENVECTORS and that's it. Thanks to all who responded. Happy New Year :-) Cordially , czernek@chemi.muni.cz From chemistry-request@server.ccl.net Mon Jan 3 14:40:20 2000 Received: from mailhost.lanl.gov (mailhost.lanl.gov [128.165.3.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA04630 for ; Mon, 3 Jan 2000 14:40:20 -0500 Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.9.3/8.9.3/(cic-5, 2/8/99)) with SMTP id LAA32455 for ; Mon, 3 Jan 2000 11:32:01 -0700 X-Sender: schrecke@t12mail.lanl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 3 Jan 2000 11:34:30 -0600 To: CHEMISTRY@ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: so effects on geometry (was: high-quality GAMESS-US basis set for iodine?) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA04631 Dear Valentin and CCL, >Does anybody know appropriate references on what effect: scalar- >relativistic or spin-orbit has more effect on geometry? There is one paper out by van Lenthe et al. where they compared scalar and spin-orbit effects on the geometry and other properties of small molecules. For instance, for I2, they find a difference in bond length of 0.019 Angstrom, one of the largest for the set of molecules considered. So, the conclusion was that the influence of spin-orbit effects on the geometry of closed- shell molecules is modest only. The same is not true, of course, for other properties including energetics or NMR. The reference is JCP 1996, 105, 6505. Besides, it is clear that one needs scalar relativistic effects to get the geometries right, cf., e.g., the classic 1988 Chem Rev. review by Pyykkö. This, then, is a point in favor of ECP basis sets for something as heavy as iodine :-) >In most cases using ECP usually gives better agreement in geometry >compared to all-electron calculations for iodine containing molecules. >For example, one may take a look at recent publications with Stuttgart >ECP basis set on iodine. Best regards, Georg -- ============================================================== Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/home/schrecke/ ==============================================================