From chemistry-request@server.ccl.net Thu Nov 23 21:54:34 2000 Received: from web9604.mail.yahoo.com (web9604.mail.yahoo.com [216.136.129.183]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA10400 for ; Thu, 23 Nov 2000 21:54:34 -0500 Message-ID: <20001124025229.2344.qmail@web9604.mail.yahoo.com> Received: from [161.142.4.9] by web9604.mail.yahoo.com; Thu, 23 Nov 2000 18:52:29 PST Date: Thu, 23 Nov 2000 18:52:29 -0800 (PST) From: sohail qamar Subject: GOOD SOFTWARE SITES. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello! Have a look at these sites.A good collection of softwares. http://nbif.org/software/software.html http://www.chem.swin.edu.au/chem_ref.html with best wishes. sohail. University Sains Malaysia. __________________________________________________ Do You Yahoo!? Yahoo! Shopping - Thousands of Stores. Millions of Products. http://shopping.yahoo.com/ From chemistry-request@server.ccl.net Fri Nov 24 01:51:47 2000 Received: from icp.ac.ru (icp.ac.ru [193.233.43.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA11230 for ; Fri, 24 Nov 2000 01:51:46 -0500 Received: from icp.ac.ru (phot2.pc.icp.ac.ru [192.168.1.93]) by icp.ac.ru (8.9.1/8.9.1) with ESMTP id JAA08677 for ; Fri, 24 Nov 2000 09:51:33 +0300 (MSK) Message-ID: <3A1E0FB9.C65934A8@icp.ac.ru> Date: Fri, 24 Nov 2000 09:50:33 +0300 From: "Mikhayl F.Budyka" Organization: Institute of Problems of Chemical Physics X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: parameters for fullerenes Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, Semiempirical methods (AM1, PM3) are known to reproduce structural parameters but overestimate greatly the heats of formation of fullerenes. Does anybody know anything about special new parametrization (PM4?) or additional parameters for PM3 for more precise calculation of the heats of formation of fullerenes? Thanks in advance, Mikhayl From chemistry-request@server.ccl.net Fri Nov 24 04:48:13 2000 Received: from batch14.uni-muenster.de (BATCH14.UNI-MUENSTER.DE [128.176.188.112]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12145 for ; Fri, 24 Nov 2000 04:48:12 -0500 Received: from asterix.uni-muenster.de (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by batch14.uni-muenster.de (Postfix) with ESMTP id 341EE1039 for ; Fri, 24 Nov 2000 10:48:02 +0100 (MEZ) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.9.3/8.9.3) with ESMTP id KAA126638 for ; Fri, 24 Nov 2000 10:48:02 +0100 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Fri, 24 Nov 2000 10:48:01 +0100 (MEZ) From: Chun Chung Chan To: chemistry@ccl.net Subject: Summary of geom opt of Se5Br2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, --------------original question---------------- We are currently working on the geometry optimization of a linear chain molecule Se5Br2 under the following conditions: G98, Rev A.6 B3LYP/6-311G opt The optimized structure takes a planar zigzag form. The bond angles range >from 93 to 96 degrees and the bond lengths of Se-Br and Se-Se are 2.45 and 2.52 angstroms, respectively. The structure looks reasonable to me and the four optimization criteria in G98 are fulfilled. However, the freq calculation shows that there are four imaginary freqs ranging from -24 to -61 cm**-1. We repeat the calculation by "opt=(calcfc,tight)" but still get more or less the same imaginary freqs. Other than trying different input structures, could any one of you please give us some hints how to get the truely optimized ground state structure. ----------------end--------------------------------- Thanks to all those who responsed to my post. It seems that the best way or the only way is to visualize the imaginary mode by molden or something similar and then slightly distort the structures along the corresponding modes and do a reoptimization. The key word nosymm might be useful as well. As a "bonus", Dr. Bruce Tattershall is so kind to suggest MPW1PW91 as an alternative to B3LYP. Below please find the reply mails: Hi Are these four negative frequencies among the first six frequencies (translational and rotational), or they are different ones? Emad ------------------ Emad Tajkhorshid http://www.ks.uiuc.edu/~emad Theoretical Biophysics Group Beckman Institute for Advanced Science and Technology 405 N. Mathews, Urbana, IL 61801 Tel: (217)244-5042 Fax: (217)244-6078 Email: emad@ks.uiuc.edu > They are the first four frequencies. OK if they are among the first six frequencies, these small negative numbers are fine. sometimes you get negative values in the first six numbers, which will not be conisdered as vibrational modes. They are related to translation and rotation of the molecule. Apart from these six numbers, you should get (3N-6) positive numbers for your molecule. If one of these (3N-6) is negative, then you are dealing with a maximum. Emad ------------------ Emad Tajkhorshid http://www.ks.uiuc.edu/~emad Theoretical Biophysics Group Beckman Institute for Advanced Science and Technology 405 N. Mathews, Urbana, IL 61801 Tel: (217)244-5042 Fax: (217)244-6078 Email: emad@ks.uiuc.edu Hello Jerry, Obviously, the frequencies you obtain are quite low. Therefore, I expect that these imaginary modes correspond to a rotation of some groups of atoms. You can check it with molden. If it is the case, there are two possibilities: whether the modes break the symmetry and then you can distort your molecule out of the plane (according to what you said the symmetry should be Cs or higher) and you reoptimise, or, knowing the normal mode (given by gaussian) you can slightly distort your molecule along the corresponding mode and reoptimise your structure. If these modes do not correspond to a small rotation (stretching, for instance), then you probably have a real transition state. I guess it would be the case for the highest frequency mode. Then, you can try again to distort your molecule along this mode, or you can try to follow the PES with an IRC calculation until you reach a minimum. I hope this help, Pascal ************************************************************************* BOULET Pascal * c/o Prof. WEBER Jacques * Universite de Geneve * departement de Chimie Physique * 30, Quai Ernest-Ansermet * CH-1211 GENEVE 4 * et * Institut de Recherche sur la Catalyse * Universite Claude Bernard LYON I * c/o Prof. CHERMETTE Henry * 43, Boulevard du 11 Novembre 1918 * F-69622 VILLEURBANNE CEDEX * * tel: (0041) (22) 702-65-77 * fax: (0041) (22) 702-65-18 * E-mail: Pascal.Boulet@chiphy.unige.ch * ************************************************************************* From chemistry-request@server.ccl.net Fri Nov 24 12:41:05 2000 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14593 for ; Fri, 24 Nov 2000 12:41:04 -0500 Received: from iqc.udg.es (ronaldo.udg.es [130.206.128.180]) by stark.udg.es (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA52233 for ; Fri, 24 Nov 2000 13:44:50 -0800 (PST) Message-ID: <3A1EA9CC.87C621F0@iqc.udg.es> Date: Fri, 24 Nov 2000 18:47:56 +0100 From: Miquel =?iso-8859-1?Q?Sol=E0?= Organization: IQC X-Mailer: Mozilla 4.7 [ca] (Win98; U) X-Accept-Language: ca MIME-Version: 1.0 To: "CCL, Computational Chemistry List" Subject: Numerical integration code Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL friends, I am looking for a code (preferably a Fortran program) that allows numerical integration of electron densities and related properties using the method designed by Becke in JCP 88 (1988) 2547 or similar. Does anyone know of some free (or nearly free) software that might accomplish these objectives? Thanks in advance. Best wishes, Miquel -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Dr. Miquel Solà Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Voice +34.972.41.89.12 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel@iqc.udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* From chemistry-request@server.ccl.net Fri Nov 24 04:48:13 2000 Received: from batch14.uni-muenster.de (BATCH14.UNI-MUENSTER.DE [128.176.188.112]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12145 for ; Fri, 24 Nov 2000 04:48:12 -0500 Received: from asterix.uni-muenster.de (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by batch14.uni-muenster.de (Postfix) with ESMTP id 341EE1039 for ; Fri, 24 Nov 2000 10:48:02 +0100 (MEZ) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.9.3/8.9.3) with ESMTP id KAA126638 for ; Fri, 24 Nov 2000 10:48:02 +0100 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Fri, 24 Nov 2000 10:48:01 +0100 (MEZ) From: Chun Chung Chan To: chemistry@ccl.net Subject: Summary of geom opt of Se5Br2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Se5Br2 continued: > From Laurence.Cuffe@ucd.ie Fri Nov 24 10:24:01 2000 Date: Thu, 23 Nov 2000 18:16:36 +0000 From: Laurence Cuffe To: Chun Chung Chan Subject: Re: CCL:geom optimization >Other than trying different input structures, could any one of you >please give us some hints how to This is what youve got to do! sorry the low frequencies -21 are probaly soft rotations but I woulfd be more concerned about the -61 one. Look at the output file and try and visualize what this vibrational mode involves if youve got visualization software such as gaussview it helps I believe molden can do this too and is free but I've not used it. Once you have visualized what the imaginary vibration is you then distort the molecule in a manner coresponding to this mode and reoptimize. Ihope this helps and is not too disconcerting Laurence Cuffe Hi, What is the symmetry of your molecule? If it's higher than C1 I would suggest you to try another optimization with NoSymm keyword. It might be that your molecule has lower symmetry than set by your initial geometry (might be nonplanar, for example), and gaussian can not lower symmetry in the course of optimization. Best regards Peeter --- Peeter Burk Jakobi 2, 51014 Tartu, Estonia Institute of Chemical Physics Phone (372-7) 375-258 Tartu University Fax (372-7) 375-264 Estonia E-mail peeter@chem.ut.ee ====================================================== > From Bruce.Tattershall@newcastle.ac.uk Fri Nov 24 10:24:11 2000 Date: Thu, 23 Nov 2000 20:09:58 +0000 (GMT) From: Bruce. Tattershall To: Chun Chung Chan Subject: Re: CCL:geom optimization I am very interested in the problem you are doing, as I am also working on rather inorganic selenium-containing molecules. Why not do a low-level calculation first, e.g. RHF/3-21G* opt followed by freq, to try to get round this bug, then push it up to DF and a bigger basis set when you have got it sorted out? I sense that current thinking is starting to favour MPW1PW91 rather than B3LYP for inorganic systems such as this, and I find that MPW1PW91/SVP is a good level to finish up at for my purposes, where SVP is Ahlrichs split-valence polarisation basis, which is built into g98. Could your problem be because you have constrained the symmetry in your geometry optimisation, e.g. to Cs because you believe your molecule is planar? If so, maybe it doesn't want to be, and this is showing up in the freq calculation. Are the negative force constants really for vibrations? I believe that the first six printed along a line of the output are for translations and rotations. These are often negative, but in my work, the values are much smaller than yours. The following line then starts to list real vibrations, which are then repeated in the table below. These have to be positive, otherwise the structure is not at a true minimum. Do you know that R.S. Laitinen at the U of Oulu, Finland, has worked on very similar Se chains, and probably knows all the problems of doing ab initio calculations on them? I do not know whether you would think it appropriate to contact him. Bruce Tattershall Personal Email: Bruce.Tattershall@newcastle.ac.uk Dr. B.W. Tattershall, Department of Chemistry University of Newcastle, Newcastle upon Tyne, England Dear Chun: Hi, To get the true optimized structure of ground state of your molecule, 1) try to animate the vibrational modes with the imaginary frequency and figure out how to deform the structure. 2) deform the structure like the vibrational mode with the highest imaginary frequency 3) and optimize the deformed structure then you will get a new minimum. Sincerely yours, Sang Yeon Lee. ------------------------------------------------------------- Prof. Sang Yeon Lee e-mail) sanglee@knu.ac.kr Dept. of Industrial Chemistry tel) +82-53-950-5583 Kyungpook Nat'l Univ. fax) +82-53-950-6594 1370 Sankyuk-dong, Puk-ku, Taegu, 702-701, S. Korea