From chemistry-request@server.ccl.net Tue Jun 27 01:31:01 2000 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA14927 for ; Tue, 27 Jun 2000 01:31:00 -0400 Received: from p17-111.dialup.UVic.CA (p17-111.dialup.UVic.CA [142.104.17.111]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id WAA178592 for ; Mon, 26 Jun 2000 22:30:36 -0700 From: Roy Jensen To: CHEMISTRY@ccl.net Subject: SUMMARY: metal halogen/sulfur clusters Date: Mon, 26 Jun 2000 22:30:34 -0700 Message-ID: X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA14930 I posted the following message a month ago. >I am looking for a method that reasonable predicts the structure of >transition metal--halogen or metal--sulfur clusters, >Metal(x)Halo/Sulfur(y) where 1<=x<=6 and 1<=y<=10. >We have Gaussian and Hyperchem available; both running on PC's. Our >goal is to compliment our expt data with reasonable predictions on >structure and stability and explain some of the trends we observe. Thanks to those who responded. I still haven't been able to get it to work as you will see in the next message. These are the responses: Prof. Alexander Bagatur'yants -- sasha@photonics.ru > may recommend you our paper >A.A. Bagatur'yants, A.A. Safonov, H. Stoll, and H.-J. Werner, "Ab initio >Relativistic Pseudopotential Study of Small Silver and Gold Sulfide Clusters >(M2S)n, n = 1 and 2," Journal of Chemical Physics, 1998, vol. 109, no. 8, >pp. 3096-3107. > >Actually, this is a real problem, which is partly discussed in the paper >cited above. Txoni -- pobmabej@sq.ehu.es > Concerning your email, we have studied ZnS small clusters. The >method >we have used is B3LYP, within DFT framework. I do not know if it will >be useful for you, but it can help. The work has been published in >Physical >Review A, vol 61, 053021 (2000). Dr. Ida N. L. Ma -- ida@ihpc.nus.edu.sg > You might like to check up papers from Prof. I. G. Dance and his >group at University of New South Wales, Australia. He has done a lot of >DFT calculations of metal-sulfur clusters which you may find useful. Valentine P. Ananikov -- val@cacr.ioc.ac.ru >Very likely you will have to use B3LYP method with ECP basis set >on transition metal and heavy halogens Br and I. You may try >b3lyp/lanl2dz or b3lyp/stuttgardt for a quick tests, both >available in Gaussian. > >Even for the simple halogen complexes of transition metals with >Br or I the error in metal-halogen bond length in order of 0.1A >is not uncommon compared to x-ray data. However, it is difficult >to distinguish between the calculations method failure and the >influence of crystalline environment. > >In general, the accuracy is good enough, but the deviations should >be treated with care. Marcel Swart -- m.swart@chem.rug.nl >use Density Functional Theory (for instance Becke88-Perdew86) which >gives quite good agreement for bond lengths/bonding energies. The >smartest program to use for this is the Amsterdam Density Functional >(ADF) program: http://www.scm.com > >Another trustworthy method is the CASPT2 approach, developed in Lund. >This can best be used with MOLCAS: http://www.teokem.lu.se/molcas/ > >Other methods can not be trusted as these two. From chemistry-request@server.ccl.net Tue Jun 27 01:31:09 2000 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA14935 for ; Tue, 27 Jun 2000 01:31:08 -0400 Received: from p17-111.dialup.UVic.CA (p17-111.dialup.UVic.CA [142.104.17.111]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id WAA117580 for ; Mon, 26 Jun 2000 22:31:00 -0700 From: Roy Jensen To: CHEMISTRY@ccl.net Subject: Help on transition metal--chlorine optimization Date: Mon, 26 Jun 2000 22:30:57 -0700 Message-ID: X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA14937 All I posted a message to the CCL a few weeks ago; a summary was just posted. DFT was the choice for geometry optimizations on transition metal--chlorine clusters (neutral and ionic). I am using Gaussian 94W and 98W however I cannot get the simplest job to run. I have tried several methods and various basis sets. Almost all fail to converge on the first step. A sample input and output file are given below. Thanks, Roy Jensen INPUT FILE ========= # UB3LYP LANL2DZ opt test Optimized geometry for FeCl. 0 2 Fe Cl 1 R1 R1=2.19 OUTPUT FILE =========== ... of initial guess= .7500 Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06. Keep R1 and R2 integrals in memory in canonical form, NReq= 727936. Integral accuracy reduced to 1.0E-05 until final iterations. Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -137.386151674 A.U. after 65 cycles Convg = .4226E-01 -V/T = 2.6548 S**2 = .8263 Annihilation of the first spin contaminant: S**2 before annihilation .8263, after .7500 Convergence failure -- run terminated. Error termination via Lnk1e in D:\G94W\l502.exe. Job cpu time: 0 days 0 hours 11 minutes 38.0 seconds. File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 (increasing 'maxcyc' and using 'novaracc' does not help) From chemistry-request@server.ccl.net Tue Jun 27 03:14:16 2000 Received: from batch16.uni-muenster.de (BATCH16.UNI-MUENSTER.DE [128.176.188.114]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA15363 for ; Tue, 27 Jun 2000 03:14:16 -0400 Received: from ASTERIX.uni-muenster.de (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by batch16.uni-muenster.de (Postfix) with ESMTP id 1106E1094; Tue, 27 Jun 2000 09:14:09 +0200 (MES) Received: (from cml@localhost) by ASTERIX.uni-muenster.de (AIX4.3/8.9.3/8.9.3) id JAA37246; Tue, 27 Jun 2000 09:14:08 +0200 From: Christian Mück-Lichtenfeld Message-Id: <200006270714.JAA37246@ASTERIX.uni-muenster.de> Subject: Tuning G98-A.9 on Power3 machines To: chemistry@ccl.net Date: Tue, 27 Jun 2000 09:14:08 +0200 (MES) Cc: cml@uni-muenster.de X-Mailer: ELM [version 2.4ME+ PL60 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Colleagues, we have just purchased the new Gaussian98 revision (A9) and had hoped to get some better performance on our IBM RS6000 260 machines, compiling with XLF6.1 and XLF7. Compiling with -O4 finishes successfully but the program ends with an 'file operation on non-existent file' error during the execution of testjobs. This does not occur when the program is compiled with -O3. We have observed that the cpu time of almost all testjobs is independent from using either the BLAS-library from the distribution or the ESSL-library. Maybe Gaussian98 does not make use of subroutines like DGEMM, which is contained in blas.F but never called from any link ? This would explain why we do not see an effect when the library is changed, because the library is not used in the program code. It would be great if someone of you who has compiled and optimized G98 Rev A9 (or A7) under similar hardware conditions could help us with the optimal compiler options and configuration for a 64 bit version on a Power3 machine. Maybe this is not the right place for such a technical question but Gaussian Inc. has not responded to any such questions (by email or fax) in the past in spite of the promised 'installation support'. Best wishes to all, Christian Mueck-Lichtenfeld ---------------------------------------------- Dr. Christian Mueck-Lichtenfeld Westfaelische Wilhelms-Universitaet Organisch-Chemisches Institut Corrensstrasse 40 D-48149 Muenster, Germany cml@uni-muenster.de | Tel +49 251 83 33301 | Fax +49 251 83 36515 ---------------------------------------------- From chemistry-request@server.ccl.net Tue Jun 27 04:00:16 2000 Received: from ifp.ifp.fr (ifp.ifp.fr [156.118.212.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA15520 for ; Tue, 27 Jun 2000 04:00:07 -0400 Received: from irsil145.ifp.fr (irsil145.ifp.fr [156.118.20.20]) by ifp.ifp.fr (8.9.3/8.9.3) with ESMTP id JAA27943; Tue, 27 Jun 2000 09:59:46 +0200 (MET DST) Received: from ifp.fr (localhost [127.0.0.1]) by irsil145.ifp.fr (8.8.5/8.8.5) with ESMTP id JAA2697741; Tue, 27 Jun 2000 09:53:04 +0200 (MDT) Sender: toulhoat@ifp.fr Message-ID: <39585D5F.56AFBD6@ifp.fr> Date: Tue, 27 Jun 2000 09:53:04 +0200 From: Herve Toulhoat Organization: Institut Francais du Petrole To: Roy Jensen CC: CHEMISTRY@ccl.net Subject: Re: CCL:SUMMARY: metal halogen/sulfur clusters References: Dear Roy, You might also be interested by the following references from my group: G. valerio, H. Toulhoat Local, gradient-corrected, and hybrid density functional calculations on Pdn clusters for n=1-6 J. Phys. Chem, 100, 26, 1996, 10827-10830 G. Valerio, H. Toulhoat "Atomic sulfur and chlorine interaction with Pdn clusters, n=1-6: a density functional study" J. Phys. Chem. A, 101, 1997, 1969-1974. P. A. Gravil and H. Toulhoat " Hydrogen, sulphur and chlorine coadsorption on Pd(111): a theoretical study of poisoning and promotion " Surf. Sci. 430 (1999) 176-191. P. A. Gravil and H. Toulhoat " Ethylene, sulphur and chlorine coadsorption on Pd(111): a theoretical study of poisoning and promotion " Surf. Sci. 430 (1999) 192-198. The first two correspond to cluster calculations at the DFT/B3LYP level. We used G94 in these studies. The two following papers are slab calculations at the DFT/PW-USPP/GGA level. We used VASP. Yours sincerely, Herve Toulhoat Roy Jensen wrote: > I posted the following message a month ago. > > >I am looking for a method that reasonable predicts the structure of > >transition metal--halogen or metal--sulfur clusters, > >Metal(x)Halo/Sulfur(y) where 1<=x<=6 and 1<=y<=10. > > >We have Gaussian and Hyperchem available; both running on PC's. Our > >goal is to compliment our expt data with reasonable predictions on > >structure and stability and explain some of the trends we observe. > > Thanks to those who responded. I still haven't been able to get it to > work as you will see in the next message. These are the responses: > > Prof. Alexander Bagatur'yants -- sasha@photonics.ru > > may recommend you our paper > >A.A. Bagatur'yants, A.A. Safonov, H. Stoll, and H.-J. Werner, "Ab initio > >Relativistic Pseudopotential Study of Small Silver and Gold Sulfide Clusters > >(M2S)n, n = 1 and 2," Journal of Chemical Physics, 1998, vol. 109, no. 8, > >pp. 3096-3107. > > > >Actually, this is a real problem, which is partly discussed in the paper > >cited above. > > Txoni -- pobmabej@sq.ehu.es > > Concerning your email, we have studied ZnS small clusters. The > >method > >we have used is B3LYP, within DFT framework. I do not know if it will > >be useful for you, but it can help. The work has been published in > >Physical > >Review A, vol 61, 053021 (2000). > > Dr. Ida N. L. Ma -- ida@ihpc.nus.edu.sg > > You might like to check up papers from Prof. I. G. Dance and his > >group at University of New South Wales, Australia. He has done a lot of > >DFT calculations of metal-sulfur clusters which you may find useful. > > Valentine P. Ananikov -- val@cacr.ioc.ac.ru > >Very likely you will have to use B3LYP method with ECP basis set > >on transition metal and heavy halogens Br and I. You may try > >b3lyp/lanl2dz or b3lyp/stuttgardt for a quick tests, both > >available in Gaussian. > > > >Even for the simple halogen complexes of transition metals with > >Br or I the error in metal-halogen bond length in order of 0.1A > >is not uncommon compared to x-ray data. However, it is difficult > >to distinguish between the calculations method failure and the > >influence of crystalline environment. > > > >In general, the accuracy is good enough, but the deviations should > >be treated with care. > > Marcel Swart -- m.swart@chem.rug.nl > >use Density Functional Theory (for instance Becke88-Perdew86) which > >gives quite good agreement for bond lengths/bonding energies. The > >smartest program to use for this is the Amsterdam Density Functional > >(ADF) program: http://www.scm.com > > > >Another trustworthy method is the CASPT2 approach, developed in Lund. > >This can best be used with MOLCAS: http://www.teokem.lu.se/molcas/ > > > >Other methods can not be trusted as these two. > -- Dr Herve TOULHOAT Directeur de Recherche Associe Group Leader, Molecular Modeling and Computational Chemistry Div. Computer Science and Applied Mathematics, IFP Director, Groupement de Recherches CNRS G1209: Dynamique Moleculaire Quantique Appliquee a la Catalyse Research Group CNRS G1209 Ab Initio Molecular Dynamics Applied to Catalysis (Scientific Partners: CNRS, IFP, Total, University of vienna, TU Eindhoven) INSTITUT FRANCAIS DU PETROLE Tel: +33-01-47-52-73-50 1 & 4 Avenue de Bois-Preau Fax: +33-01-47-52-70-22 92852 RUEIL-MALMAISON Cedex FRANCE E-mail: herve.toulhoat@ifp.fr Visit IFP Website at http://www.ifp.fr From chemistry-request@server.ccl.net Tue Jun 27 05:31:57 2000 Received: from mailhost.univ-orleans.fr (root@dns.univ-orleans.fr [194.167.30.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA15938 for ; Tue, 27 Jun 2000 05:31:56 -0400 Received: from univ-orleans.fr (tourmalet.univ-orleans.fr [193.49.95.21]) by mailhost.univ-orleans.fr (8.9.3/jtpda-5.3.1) with ESMTP id LAA26363 for ; Tue, 27 Jun 2000 11:31:47 +0200 Message-ID: <3958743C.7B0BFEE8@univ-orleans.fr> Date: Tue, 27 Jun 2000 11:30:37 +0200 From: nicolas baurin X-Mailer: Mozilla 4.6 [fr] (Win95; I) X-Accept-Language: fr MIME-Version: 1.0 To: chemistry@ccl.net Subject: data set for QSAR tool evaluation Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello to the CCL community, In order to fully evaluate a new soft tool designed to derive QSAR, we're looking for a dataset of around 100 molecules which is considered as a standard. If anyone could point us to references or,better, websites. Even better will be a dataset with structures and activities available on the web (.sdf or similar). Cordialement, -- Nicolas Baurin Doctorant Institut de Chimie Organique et Analytique, UPRES-A 6005 Université d'Orléans, BP 6759 45067 ORLEANS Cedex 2, France Tel: (33+) 2 38 49 45 77 From chemistry-request@server.ccl.net Tue Jun 27 06:38:51 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA16266 for ; Tue, 27 Jun 2000 06:38:41 -0400 Received: (qmail 28432 invoked from network); 27 Jun 2000 10:36:19 -0000 Received: from titanas.chemistry.upatras.gr (150.140.180.134) by nic.upatras.gr with SMTP; 27 Jun 2000 10:36:19 -0000 Received: (qmail 12749 invoked from network); 27 Jun 2000 10:42:28 -0000 Received: from orion.chemistry.upatras.gr (HELO chemistry.upatras.gr) (150.140.180.144) by titanas.chemistry.upatras.gr with SMTP; 27 Jun 2000 10:42:28 -0000 Message-ID: <395885E6.49DA2DB7@chemistry.upatras.gr> Date: Tue, 27 Jun 2000 13:45:58 +0300 From: Panaghiotis Karamanis X-Mailer: Mozilla 4.72 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: NH2CCCCNO2 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Does anybody know the structure of NH2CC-CCNO2 (bond lengths, angles, symetry) or a database where i can find any information about it? Thanks From chemistry-request@server.ccl.net Tue Jun 27 08:38:41 2000 Received: from linux2.ipc.pku.edu.cn (mao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA17576 for ; Tue, 27 Jun 2000 08:38:37 -0400 Received: from localhost (mao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id UAA24440; Tue, 27 Jun 2000 20:44:45 +0800 Date: Tue, 27 Jun 2000 20:44:45 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" cc: PDB List Subject: Molsee 1.0 released Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, all, Molsee is a GUI front end to control rasmol, now it has some new features, if you want use it, go here: http://mdl.ipc.pku.edu.cn/software/molsee.html What can Molsee do? 1.Browse your molecules in directory tree, and tell Ramsol to display them, no need to type the file name. 2.Reserve your display mode. It is very useful when you want to view many molecules via same way. For example,if you want to view many deferent conformations of one molecule. 3.Automatically run a script while loading every molecule. Automatically remember what you have done for each molecule, and show them again when you load this molecule again. It is very useful when you want to compare many molecules' special site, for example, active site and binding site. 4.Select atoms via a GUI, completely have the same function as rasmol, but no need to remember so many selection commands in rasmol. 5.Label the selected atom via GUI. 6.Color the selected atom via GUI. 7.If you use the "select" dialog box and other dialog box together, for example,the "Display Mode" dialog box, you almost can display atoms in any mode that you can do in ramsol in a very convenient way. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 From chemistry-request@server.ccl.net Tue Jun 27 10:44:45 2000 Received: from mail.sun.ac.za (mail.sun.ac.za [146.232.128.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18367 for ; Tue, 27 Jun 2000 10:44:42 -0400 Received: from akad.sun.ac.za ([146.232.80.254]) by mail.sun.ac.za with esmtp (Exim 2.10 #1) id 136wbD-0000Oq-00 for Chemistry@ccl.net; Tue, 27 Jun 2000 16:44:27 +0200 Received: from SUN_AKAD/SpoolDir by AKAD.SUN.AC.ZA (Mercury 1.47); 27 Jun 00 16:44:28 +0200 Received: from SpoolDir by SUN_AKAD (Mercury 1.47); 27 Jun 00 16:44:01 +0200 From: "SA KUEHL" Organization: Stellenbosch University To: Chemistry@ccl.net Date: Tue, 27 Jun 2000 16:44:00 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: CI subroutine Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12) Message-Id: Attention users, Does anyone know if there is available a CI routine which can calculate transition dioples/oscillator strengths for singles, doubles and triples using the output from Hyperchem log files. A singles only treatment in Hyperchem does provide this information but strongly allowed observed transitions are given a 0 oscillator strength by this method. Literature points to extensive CI mixing and this brings out the true intensities. Scott Kuehl Institute for Polymer Science University of Stellenbosch Stellenbosch South Africa From chemistry-request@server.ccl.net Tue Jun 27 12:39:51 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA19005 for ; Tue, 27 Jun 2000 12:39:51 -0400 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Tue, 27 Jun 2000 11:39:39 -0500 Message-ID: <001801bfe055$f9799500$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "Roy Jensen" , References: Subject: Re: CCL:Help on transition metal--chlorine optimization Date: Tue, 27 Jun 2000 11:37:24 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 You may try the following: 1.(a) vshift=500 or more if energy is oscillating, or (b) scf=qc 2. generate the initial guess using UHF calculation and start dft from that guess. Good luck __________________________________ Tapas Kar Department of Chemistry 1245 Lincoln Dr #146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485 (Office)/6433(Lab) Fax:618-453-6408 Email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: Roy Jensen To: Sent: Tuesday, June 27, 2000 12:30 AM Subject: CCL:Help on transition metal--chlorine optimization > All > > I posted a message to the CCL a few weeks ago; a summary was just > posted. DFT was the choice for geometry optimizations on transition > metal--chlorine clusters (neutral and ionic). > > I am using Gaussian 94W and 98W however I cannot get the simplest job > to run. I have tried several methods and various basis sets. Almost > all fail to converge on the first step. A sample input and output file > are given below. > > Thanks, > Roy Jensen > > > INPUT FILE > ========= > # UB3LYP LANL2DZ opt test > > Optimized geometry for FeCl. > > 0 2 > Fe > Cl 1 R1 > > R1=2.19 > > > OUTPUT FILE > =========== > >... > of initial guess= .7500 > Requested convergence on RMS density matrix=1.00E-08 within 64 > cycles. > Requested convergence on MAX density matrix=1.00E-06. > Keep R1 and R2 integrals in memory in canonical form, NReq= > 727936. > Integral accuracy reduced to 1.0E-05 until final iterations. > Problem detected with inexpensive integrals. > Switching to full accuracy and repeating last cycle. > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(UB+HF-LYP) = -137.386151674 A.U. after 65 cycles > Convg = .4226E-01 -V/T = 2.6548 > S**2 = .8263 > Annihilation of the first spin contaminant: > S**2 before annihilation .8263, after .7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in D:\G94W\l502.exe. > Job cpu time: 0 days 0 hours 11 minutes 38.0 seconds. > File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= > 1 > > > (increasing 'maxcyc' and using 'novaracc' does not help) > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Jun 27 10:49:32 2000 Received: from email.guomai.sh.cn (shpgjggzli@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18411 for ; Tue, 27 Jun 2000 10:49:28 -0400 Received: from guomai.sh.cn ([202.101.13.104]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0FWT00IMKIZR2K@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Tue, 27 Jun 2000 22:59:53 +0800 (CST) Date: Tue, 27 Jun 2000 22:57:27 +0800 From: Yubo Fan Subject: Oh Symmetry To: CHEMISTRY@ccl.net Message-id: <3958C0D7.85A9D423@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.73 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, everyone, I have a Keggin structure metal cluster anion, which has a Oh symmetry >from its Monocrystal XRD. The problem is G98 couldn't get its Oh symmetry when I do geometry optimization. Could anyone help me to write the right Z-Matrix orientation, which can indicate the symmetry. I attach the PDB file below. Thanks in advance Y. Fan COMPND Mo6O19.pdb HETATM 1 O 0.000 0.000 0.000 HETATM 2 Mo 0.000 2.393 0.000 HETATM 3 Mo -2.393 0.000 0.000 HETATM 4 Mo 0.000 0.000 2.393 HETATM 5 Mo 0.000 -2.393 0.000 HETATM 6 Mo 2.393 0.000 0.000 HETATM 7 Mo 0.000 0.000 -2.393 HETATM 8 O 0.000 4.123 0.000 HETATM 9 O -4.123 0.000 0.000 HETATM 10 O 0.000 0.000 4.123 HETATM 11 O 0.000 -4.123 0.000 HETATM 12 O 4.123 0.000 0.000 HETATM 13 O 0.000 0.000 -4.123 HETATM 14 O -1.887 1.887 0.000 HETATM 15 O -1.887 0.000 1.887 HETATM 16 O 0.000 1.887 1.887 HETATM 17 O 1.887 -1.887 0.000 HETATM 18 O 1.887 0.000 -1.887 HETATM 19 O 0.000 -1.887 -1.887 HETATM 20 O 1.887 1.887 0.000 HETATM 21 O 0.000 1.887 -1.887 HETATM 22 O -1.887 0.000 -1.887 HETATM 23 O -1.887 -1.887 0.000 HETATM 24 O 0.000 -1.887 1.887 HETATM 25 O 1.887 0.000 1.887 CONECT 2 8 14 16 20 CONECT 2 21 CONECT 3 9 14 15 22 CONECT 3 23 CONECT 4 10 15 16 24 CONECT 4 25 CONECT 5 11 17 19 23 CONECT 5 24 CONECT 6 12 17 18 20 CONECT 6 25 CONECT 7 13 18 19 21 CONECT 7 22 CONECT 8 2 CONECT 9 3 CONECT 10 4 CONECT 11 5 CONECT 12 6 CONECT 13 7 CONECT 14 2 3 CONECT 15 3 4 CONECT 16 2 4 CONECT 17 5 6 CONECT 18 6 7 CONECT 19 5 7 CONECT 20 2 6 CONECT 21 2 7 CONECT 22 3 7 CONECT 23 3 5 CONECT 24 4 5 CONECT 25 4 6 END -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Tue Jun 27 11:17:11 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA18653 for ; Tue, 27 Jun 2000 11:17:11 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA08069; Tue, 27 Jun 2000 11:22:56 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 27 Jun 2000 11:15:04 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V5.2-32 #33820) with ESMTP id <0FWT0010TJY19R@lvlmail.unitedcatalysts.com>; Tue, 27 Jun 2000 11:20:25 -0400 (EDT) Received: by LVLXCH01 with Internet Mail Service (5.5.2650.21) id ; Tue, 27 Jun 2000 11:15:11 -0400 Content-return: allowed Date: Tue, 27 Jun 2000 11:15:09 -0400 From: "Shobe, Dave" Subject: RE: Help on transition metal--chlorine optimization To: "'Roy Jensen'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D6383B5@LVLXCH01> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA18654 Some tricks to aid convergence: 1. Use a single-zeta basis set first, then use guess=read to import this into the double-zeta calculation. This simplifies the "vector space" in which the wave function has to be found. 2. Sometimes using a shorter than equilibrium bond length as the starting geometry helps. This produces a stronger interaction between the atoms. 3. Once you have a decent wavefunction, use vshift to prevent it from drifting astray. You might also want to make a copy of the .chk file once you have a good wavefunction, so that you can go back to it later. 4. Even with the above tricks, 64 cycles is usually far too few. Maxcyc=500 is more like it. One more thing: it's very easy to end up with a low-lying excited state with this kind of molecule. If you know where the electrons are "supposed" to be, you can look at the population analysis (you may need pop=full, which I should warn you generates tons of output) to see if the right orbitals are occupied. Also, the stable command can check for some kinds of spurious states. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. -----Original Message----- From: Roy Jensen [mailto:royj@uvic.ca] Sent: Tuesday, June 27, 2000 1:31 AM To: CHEMISTRY@ccl.net Subject: CCL:Help on transition metal--chlorine optimization All I posted a message to the CCL a few weeks ago; a summary was just posted. DFT was the choice for geometry optimizations on transition metal--chlorine clusters (neutral and ionic). I am using Gaussian 94W and 98W however I cannot get the simplest job to run. I have tried several methods and various basis sets. Almost all fail to converge on the first step. A sample input and output file are given below. Thanks, Roy Jensen INPUT FILE ========= # UB3LYP LANL2DZ opt test Optimized geometry for FeCl. 0 2 Fe Cl 1 R1 R1=2.19 OUTPUT FILE =========== >... of initial guess= .7500 Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06. Keep R1 and R2 integrals in memory in canonical form, NReq= 727936. Integral accuracy reduced to 1.0E-05 until final iterations. Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -137.386151674 A.U. after 65 cycles Convg = .4226E-01 -V/T = 2.6548 S**2 = .8263 Annihilation of the first spin contaminant: S**2 before annihilation .8263, after .7500 Convergence failure -- run terminated. Error termination via Lnk1e in D:\G94W\l502.exe. Job cpu time: 0 days 0 hours 11 minutes 38.0 seconds. File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 (increasing 'maxcyc' and using 'novaracc' does not help) -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Jun 27 11:49:37 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA18787 for ; Tue, 27 Jun 2000 11:49:36 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA04016; Tue, 27 Jun 2000 08:46:02 -0700 (PDT) Received: from osman-pc.msi.com(146.202.7.202) by mailhost.msi.com via smap (V2.0) id xma004007; Tue, 27 Jun 00 08:45:50 -0700 Message-Id: <4.2.0.58.20000627082041.00d95530@146.202.6.217> X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Tue, 27 Jun 2000 08:32:33 -0500 To: Vidana Epa , CHEMISTRY@ccl.net, osman@msi.com (Osman F. Guner) From: "Osman F. Guner" Subject: Summary: Examples for late drug candidate failures due to ADME In-Reply-To: <200006180629.QAA19196@tigger.pp.molsci.csiro.au> References: <200005152019.NAA06257@mailhost.msi.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_4991887==_.ALT" --=====================_4991887==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Dear Vidana: I received only one response to my original query, but here is the results= =20 of my search on this topic. I will also post this to CCL as a summary. Thalidomide: Sleep-inducing drug found to produce skeletal defects in developing=20 fetuses. It was sold without prescription in Europe from 1957 to 1961, when= =20 its use by pregnant women was correlated with a high incidence of babies=20 born with shortened, malformed limbs (c.8,000 worldwide). This discovery=20 stimulated the adoption of strict regulations in the testing of new drugs=20 in the U.S. (ref: http://www.encyclopedia.com/articles/12773.html) ADVERSE DRUG REACTIONS MAY CAUSE OVER 100,000 DEATHS AMONG HOSPITALIZED=20 PATIENTS EACH YEAR http://www.ama-assn.org/sci-pubs/sci-news/1998/snr0415.htm#jma71005 The Safety of Newly Approved Medicines: Do Recent Market Removals Mean=20 There Is a Problem? http://jama.ama-assn.org/issues/v281n18/full/jsc80437.html Since 1980, a total of 13 products have been withdrawn from the US market=20 for safety reasons http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc80437_t1.html http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc80437_f1.html demonstrates an apparent increase in the number of withdrawals in 1997 and= =20 1998 when the drugs are analyzed by the year of withdrawal. But when the same data are displayed by the year in which the drug was=20 approved, rather than the date of removal=20 (http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc80437_f2.html), no such= =20 clustering is apparent. Posicor=AE (Mibefradil) for Hypertension Withdrawn in U.S. 06/08/98 http://pharmacology.about.com/health/pharmacology/library/98news/bln0608a.ht= m Physicians React to News About Mibefradil http://pharmacotherapy.medscape.com/jobson/MedTrib/interncard/1998/v39.n13/P= =20 hysiciansReacttoNewsAbout.html Voluntary Market Withdrawal of DURACT (bromfenac sodium capsules) http://pharminfo.com/medwatch/mwrpt47.html WYETH-AYERST LABORATORIES ANNOUNCES THE WITHDRAWAL OF DURACT FROM THE MARKET http://pharminfo.com/medwatch/mwrpt46.html FDAMA Proposed List of Agents Not to be Compounded Due to Withdrawal For=20 Safety/Efficacy Concerns http://www.ijpc.com/chart.html At 06:29 PM 6/18/00 +1000, Vidana Epa wrote: >Dear Dr. Guner, > > I am very interested to know what examples you found from >your query to CCL. >Thanks very much. > >Best regards, > >Vidana. > > > > > > Are there any famed examples of late failures of drug candidates (or > > drugs)? Any additional information and/or references related to the= cost > > associated with those failures will also be useful. This is for a > > preliminary research on a potential symposium. I will be happy to > > summarize the responses to the list. > > > > Thx...Osman > > --- > > > > > > > > > > > > >Vidana C. Epa > >Biomolecular Research Institute, >343 Royal Parade, >Parkville, Vic. 3052, >AUSTRALIA. > > >Tel: (61) - 3 - 9662 - 7300 >Fax: (61) - 3 - 9662 - 7301 > >email: Vidana.Epa@hsn.csiro.au --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com=20 --=====================_4991887==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Vidana:

I received only one response to my original query, but here is the results of my search on this topic.  I will also post this to CCL as a summary.

Thalidomide:
Sleep-inducing drug found to produce skeletal defects in developing fetuses. It was sold without prescription in Europe from 1957 to 1961, when its use by pregnant women was correlated with a high incidence of babies born with shortened, malformed limbs (c.8,000 worldwide). This discovery stimulated the adoption of strict regulations in the testing of new drugs in the U.S.  (ref: http://www.encyclopedia.com/articles/12773.html)

ADVERSE DRUG REACTIONS MAY CAUSE OVER 100,000 DEATHS AMONG HOSPITALIZED PATIENTS EACH YEAR
http://www.ama-assn.org/sci-pubs/sci-news/1998/snr0415.h= tm#jma71005

The Safety of Newly Approved Medicines: Do Recent Market Removals Mean There Is a Problem?
http://jama.ama-assn.org/issues/v281n18/full/jsc80437.ht= ml

Since 1980, a total of 13 products have been withdrawn from the US market for safety reasons
http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc80437= _t1.html

http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc80437_f1.= html
demonstrates an apparent increase in the number of withdrawals in 1997 and 1998 when the drugs are analyzed by the year of withdrawal.

But when the same data are displayed by the year in which the drug was approved, rather than the date of removal (http://jama.ama-assn.org/issues/v281n18/fig_tab/jsc8043= 7_f2.html), no such clustering is apparent.

Posicor=AE (Mibefradil) for Hypertension Withdrawn in U.S. 06/08/98
http://pharmacology.about.com/health/pharmacology/librar= y/98news/bln0608a.htm

Physicians React to News About Mibefradil
http://pharmacotherapy.medscape.com/jobson/MedTrib/inter= ncard/1998/v39.n13/PhysiciansReacttoNewsAbout.html

Voluntary Market Withdrawal of DURACT (bromfenac sodium capsules)
http://pharminfo.com/medwatch/mwrpt47.html

WYETH-AYERST LABORATORIES ANNOUNCES THE WITHDRAWAL OF DURACT FROM THE MARKET
http://pharminfo.com/medwatch/mwrpt46.html

FDAMA Proposed List of Agents Not to be Compounded Due to Withdrawal For Safety/Efficacy Concerns
http://www.ijpc.com/chart.html



At 06:29 PM 6/18/00 +1000, Vidana Epa wrote:

Dear Dr. Guner,

        I am very interested to know what examples you found from
your query to CCL.
Thanks very much.

Best regards,

Vidana.


>
> Are there any famed examples of late failures of drug candidates (or
> drugs)?  Any additional information and/or references related to the cost
> associated with those failures will also be useful.  This is for a
> preliminary research on a potential symposium.  I will be happy to
> summarize the responses to the list.
>
> Thx...Osman
> ---
>
>
>
>




Vidana C. Epa   

Biomolecular Research Institute,
343 Royal Parade,
Parkville, Vic. 3052,
AUSTRALIA.


Tel:   (61) - 3 - 9662 - 7300
Fax:   (61) - 3 - 9662 - 7301

email: Vidana.Epa@hsn.csiro.au 

---
Osman F. G=FCner, Ph.D.
Director,  Lead Identification & Optimization
Molecular Simulations Inc.   (858) 799-5341
osman@msi.com        http://www.msi.com --=====================_4991887==_.ALT-- From chemistry-request@server.ccl.net Tue Jun 27 13:09:43 2000 Received: from jmlopez.fam.cie.uva.es (aguado@jmlopez.fam.cie.uva.es [157.88.38.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19392 for ; Tue, 27 Jun 2000 13:08:15 -0400 Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.9.1/8.9.1) id CAA09754 for CHEMISTRY@ccl.net; Thu, 13 Jan 2000 02:40:34 +0100 Date: Thu, 13 Jan 2000 02:40:34 +0100 From: Andres Aguado Message-Id: <200001130140.CAA09754@jmlopez.fam.cie.uva.es> To: CHEMISTRY@ccl.net Subject: Oxide surfaces... Dear all, Could someone point me some review/report general articles on the chemical/physical properties of oxide surfaces (MgO and ferroelectric perovskites), at both experimental and theoretical levels? Thanks in advance. A. Aguado. From chemistry-request@server.ccl.net Tue Jun 27 15:38:30 2000 Received: from shiva.hunter.cuny.edu (shiva.hunter.cuny.edu [146.95.128.96]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20975 for ; Tue, 27 Jun 2000 15:38:30 -0400 Received: from shiva (shiva [146.95.128.96]) by shiva.hunter.cuny.edu (8.9.3/8.9.3) with ESMTP id PAA19628 for ; Tue, 27 Jun 2000 15:38:38 -0400 (EDT) Date: Tue, 27 Jun 2000 15:38:37 -0400 (EDT) From: AM To: CHEMISTRY@ccl.net Subject: Do you know a Computational Chemistry Consultant? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, ACS NY/NJ section, Younger Chemists Committee is looking for a Computational Chemist who is in Consulting business. If anyone knows (or is) such a person, we'd really like to hear from you! We are planning 3 semninars this Fall for postdocs/grad/undergrad students in NYC metropolitan area. Please, reply to this email directly, I am not CCL subscriber at the moment.. Regards, Artem Masunov __ ___________ Artem.Masunov@usa.net;tel 212-772-5751;fax212-772-5332 / \ / __ __ \ text pager: instantmessage@bigfoot.com (max. 120 char.) / \/\ \ \ \ \ \ Chemistry Department, Hunter College, City U. of NY / /\ \ \ \ \ \ \ \ 695 Park Avenue, New York, NY 10021 / ____ \ \ \ \ \ \ \ --------------------------------------------------- /__/\ _/\ _\ \ _\ \ _\ \ _\ FORGIVE MY NONSENSE AS I ALSO FORGIVE THOSE \ _\/ \/__/\ __/\ __/\ __/ WHO THINK THEY TALK SENSE -- ROBERT FROST From chemistry-request@server.ccl.net Tue Jun 27 15:33:43 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20863 for ; Tue, 27 Jun 2000 15:33:43 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA12658; Tue, 27 Jun 2000 12:30:27 -0700 (PDT) Received: from unknown(146.202.10.179) by mailhost.msi.com via smap (V2.0) id xma012648; Tue, 27 Jun 00 12:30:06 -0700 Message-Id: <4.2.0.58.20000627123111.00a51ca0@146.202.6.218> X-Sender: nxg@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Tue, 27 Jun 2000 12:38:41 +0100 To: Andres Aguado From: nxg Subject: Re: CCL:Oxide surfaces... Cc: CHEMISTRY@ccl.net In-Reply-To: <200001130140.CAA09754@jmlopez.fam.cie.uva.es> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello, Check these articles by H.J. Freund. Faraday Discussions, no 114, pages 1-31, 1999 Report on Progress in Physics, March 1996, Vol 59 (no. 3) pages 283-347 -Niri Govind At 02:40 AM 1/13/00 +0100, you wrote: >Dear all, > >Could someone point me some review/report general articles on the >chemical/physical properties of oxide surfaces (MgO and ferroelectric >perovskites), at both >experimental and theoretical levels? > >Thanks in advance. > >A. Aguado. > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > >