From chemistry-request@server.ccl.net Mon Feb 14 05:44:11 2000 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA11206 for ; Mon, 14 Feb 2000 05:44:08 -0500 Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.3]) by netra.ksu.edu.sa (8.9.0/8.9.0) with ESMTP id MAA05252 for ; Mon, 14 Feb 2000 12:41:31 -0300 (Etc/GMT) Received: from localhost (azhary@localhost) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id MAA08097 for ; Mon, 14 Feb 2000 12:39:55 -0300 (GMT) Date: Mon, 14 Feb 2000 12:39:54 -0300 (GMT) From: "Adel Abbas Ali Elazhary Sci. College" X-Sender: azhary@sun1 To: chemistry@ccl.net Subject: basis set for metal complexes (summary) In-Reply-To: Message-ID: 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 FAA11207 Dear ccl members: About two weeks ago a I sent a question about basis set for metals. I received more requests to summerize than answers. The following are my original question and the only answer I got. Best regards, Adel El-Azhary ======================= original question ====================== Dear ccl members" I am doing DFT calculations on metal complexes with organic molecules and do not know what basis set should I use. Is there any study about basis set effect on DFT calculated geometry or ir spectrum of metal complexes. It might even help if someone suggest a test molecule for which its vibrational spectrum (especially the bands corresponding to the metal vibrations) are known. Thanking you in advance. Best regards, ======================= only answer ! ============================ Calculating metal complexes there is not much choice of basis sets. Using Gaussian, 6-311G is defined for 3d metals, but not for 4d and 5d. 4d and 5d are best calculated with pseudo potentials, which do take care of relativistic effects. LanL2DZ is best known, but you can also choose the Stuttgart Potentials (which are said to be implemented in G98, but we tend to have problems with the internal basis sets and prefer to specify in the input line. You can get basis sets input files on the net (www.uni-stuttgart.de , than searching for the theochem group) For 3d metals you have the choice of 6-311 and LanL2DZ or SDD - my experience with copper complexes is, that 6-311 give slighty better geometries, but do have convergence problems. Generally I do use mixed basis sets - e.g. 6-31(d) for the ligand and LanL2DZ or 6-311G for the metal centre. Calculating frequencies - well, with pseudopotentials there is no direct way to calculate them. They are calculating by searching systematically the surface, which is a somewhat time-consuming procedure. Best wishes Achim Achim Lienke PostDoctoral Research Fellow Anorganisch Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 270 D 69120 Heidelberg Phone: ++ 49 6221 54 86 53 Fax: ++ 49 6221 54 66 17 =============================== end of the only answer ! ============= From chemistry-request@server.ccl.net Mon Feb 14 07:25:21 2000 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA12404 for ; Mon, 14 Feb 2000 07:25:20 -0500 Received: from PC-Pascal.unige.ch ([129.194.52.113]) by sc2a.unige.ch (PMDF V5.2-32 #37940) with SMTP id <01JLWBKL1IZO002DGW@sc2a.unige.ch> for chemistry@www.ccl.net; Mon, 14 Feb 2000 12:20:41 MET-DST Date: Mon, 14 Feb 2000 12:20:40 +0100 From: pascal boulet Subject: Oscillator strengths To: ccl Message-id: <00f401bf76dd$879370a0$7134c281@PC-Pascal.unige.ch> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Mailer: Microsoft Outlook Express 4.72.3110.5 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-Priority: 3 X-MSMail-priority: Normal Dear CCL's I am interested in the calculation of vertical excitations within the Time-Dependent Density Functional Response Theory. I have found many articles discussing the accuracy of various functionals to reproduce excitation energies. But I could not find any article dealing with the reliability of oscillator strengths! Could someone give me a reference? Thank in advance, Pascal ****************************************************************** Pascal BOULET Pascal.Boulet@chiphy.unige.ch Département de Chimie-Physique Université de Genève 30, Quai Ernest-Ansermet CH-1211 Genève 4 tel: (+41) 22 702 65 77 or (+41) 22 702 65 32 fax: (+41) 22 702 65 18 and Université Claude Bernard Lyon 1 43, Bd du 11 Novembre 1918 69622 Villeurbanne Cedex France **************************************************************** From chemistry-request@server.ccl.net Mon Feb 14 07:36:59 2000 Received: from mserv3.dl.ac.uk (root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA12461 for ; Mon, 14 Feb 2000 07:36:58 -0500 Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id LAA21403 for ; Mon, 14 Feb 2000 11:33:03 GMT Sender: H.J.J.VanDam@dl.ac.uk Message-ID: <38A7E4FB.AB85B548@dl.ac.uk> Date: Mon, 14 Feb 2000 11:20:28 +0000 From: Huub van Dam Organization: CCLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Chemical Datamanagement Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I have been asked to give a talk on scientific data management to bring forward the requirements of the chemical community. So I would like to invite any comments or references on topics like: - Datastorage: What data do we need to store, how much of it and for how long? - Interoperability: Different data formats and programs and to make everything (not) work together. - Visualisation: What and how to visualise (and what does it show)? - Analysis: Storing tons of data is one thing but how to extract meaningful information from all that? What kind of analysis do we want to do? - Any other aspect that comes to mind. Please send emails to me directly, I will summarise. Many thanks, Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== From chemistry-request@server.ccl.net Mon Feb 14 15:07:37 2000 Received: from iris.inc.bme.hu (iris.inc.bme.hu [152.66.63.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA15219 for ; Mon, 14 Feb 2000 15:07:35 -0500 Received: from localhost (dino@localhost) by iris.inc.bme.hu (8.9.3/8.9.3) with ESMTP id UAA23198 for ; Mon, 14 Feb 2000 20:05:29 +0100 (BUD) Date: Mon, 14 Feb 2000 20:05:28 +0100 From: Szieberth Denes To: CHEMISTRY@ccl.net Subject: quad motherboard Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone any test data or experience with four-processor intel pc -s? I'm especially interrested in the scalability of DFT geometry optimizations/freqency calculations with Gaussian 94/98 on machines like that. regards, Denes Szieberth PhD student Technical University of Budapest Hungary From chemistry-request@server.ccl.net Mon Feb 14 18:15:51 2000 Received: from darwin.ntu.edu.au (darwin.ntu.edu.au [138.80.128.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA16218 for ; Mon, 14 Feb 2000 18:15:48 -0500 Received: (qmail 13167 invoked from network); 14 Feb 2000 22:10:52 -0000 Received: from quoll.ntu.edu.au (138.80.63.13) by darwin.ntu.edu.au with SMTP; 14 Feb 2000 22:10:52 -0000 Received: by quoll.ntu.edu.au; (5.65/1.1.8.2/09Aug94-1121AM) id AA12579; Tue, 15 Feb 2000 08:02:43 +0930 Date: Tue, 15 Feb 2000 08:02:43 +0930 From: Brian Salter-Duke To: chemistry@ccl.net Subject: Basis sets. Message-Id: <20000215080243.A12569@quoll.ntu.edu.au> Mail-Followup-To: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.6i I have a comment and a request leading from it. Increasingly I read about basis sets such as 6-31G for 3rd row atoms, 6-311G for transition 1st row metals. These of course are not strictly 6-31G and 6-311G. We have the Binning-Curtiss basis fro Ga-Kr, and the Maclean-Chandler basis for 2nd row which are both labelled 6-31G. The 6-311G basis for transition metals is the Wachters basis. G2 for Ga-Kr uses another basis which is labelled 6-311G. This is unfortunate. The correct name should be used. It also clouds my question in that it leads people to believe that say the proper Pople 6-31G for F is, in some sense, equivalent to the McLean-Chandler basis for Cl. My question is this - what criteria could we use to test whether a basis set for one row is equivalent to a basis set for another row? I have thought hard about this and can not come up with a satisfactory answer. You might say it is meaningless and so it is in a sense. But in developing say G2 theory or G3 theory for a set of elements where it has not previously been used one has to address it by selecting basis sets that are in some sense equivalent to those used in the theory previously for other atoms. Thus Curtiss and coworkers developed the basis used for Ga-Kr and labelled it 6-311G, but it is actially, from memory, [62111111,3331111,41]. I will post a summary of responses. Regards, Brian Duke. -- Associate Professor Brian Salter-Duke (Brian Duke) Chemistry, Faculty of Science, IT and Education, Northern Territory University, Darwin, NT 0909, Australia. Phone (61) (0)8-89466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au From chemistry-request@server.ccl.net Mon Feb 14 18:48:54 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA16437 for ; Mon, 14 Feb 2000 18:48:53 -0500 Received: from iaf.uquebec.ca ([198.168.44.39]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 288 for ; Mon, 14 Feb 2000 17:42:09 -0500 Message-ID: <38A88536.30F2296E@iaf.uquebec.ca> Date: Mon, 14 Feb 2000 17:44:07 -0500 From: "Jianhui Wu" Organization: INRS-IAF X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dock4.0 + InsightII, charge, orientaion tried 0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, (1). Assigning charges using insightII I am using DOCK 4.0.1. Unfortunately, I have to use InsightII instead of Sybyl to assign charges for ligands. My question is what forcefield is more suitable for DOCK 4.0.1? The receptor is assigned with Amber charge. However, it is very difficult to assign Amber charge for a large database (organic compounds) automatically. Therefore, I try to use CVFF (consistent-valence forcefield). The docking result is reasonable. However, I do not like the idea to mix two forcefield in one calculation. (CVFF charge and Amber charge are derived quite differently). At second thoughts, I might just go on doing it as far as the result is good. But I am really not sure about it. Any suggestion would be greatly appreciated. By the way, regarding Gasteiger charges computed by Sybyl, is there freeware that can produce similar charges at similar speed? (2). Orientation tried 0, Orientation score 0, why? Again, it is DOCK 4.0.1. When I dock a single ligand, I get a message that 0 orientation was tried and 0 orientation was scored (in fact, it happens a dozens times to me now). Yes, the ligand is small related to the binding site defined. I thought this is the reason for that until I encounter an even smaller molecule which DOCK processed it and scored it. How come DOCK kick that first molecule out without even try one orientaion? (The structure is correct. The min & max heavy atoms are correctly set). Thanks a lot for your help. Regards, Jian Hui Wu email: Jianhui_Wu@IAF.Uquebec.ca From chemistry-request@server.ccl.net Mon Feb 14 19:56:05 2000 Received: from sirocco.cc.mcgill.ca (sirocco.CC.McGill.CA [132.206.27.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA16794 for ; Mon, 14 Feb 2000 19:56:05 -0500 Received: from ariya430 (ariya430.Chem.McGill.CA [132.206.175.28]) by sirocco.cc.mcgill.ca (8.9.1/8.9.1) with SMTP id SAA11552 for ; Mon, 14 Feb 2000 18:51:20 -0500 (EST) Message-Id: <200002142351.SAA11552@sirocco.cc.mcgill.ca> From: "Alexei Khalizov" Organization: Chemistry Dept., McGill University To: chemistry@ccl.net Date: Mon, 14 Feb 2000 18:51:16 -0500 MIME-Version: 1.0 Content-type: text/enriched; charset=ISO-8859-1 Content-transfer-encoding: Quoted-printable Subject: How can one calculate reaction rate constant? Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) 0100,0100,0100Times New RomanDear CCLers, I would like to calculate rate constant k for bimolecular reaction A + B -> AB. I have found transition state and proved that it really connects reagents and products (G98w, GAMESS). According to RRKM the simplest expression for calculation of rate constant k is k =3D (kB*T/h)(Q=92=92/Qa*Qb) exp(-Eo/RT), where kB is Boltzmann=92s constant; Q=92=92, Qa and Qb are partition functions for TS and reagents A and B; Eo =96 difference in zero point energies of TS and reagents. Question: what units and what measure does this rate constant k have? Simple evaluation gives units of [s-1], but being a bimolecular it is expected to have units of [M-1s-1], [cm3 molecules-1 s-1] or such. How can we account for this? Sincerely, Alexei Khalizov, Balakrishnan Viswanathan ------------------------- Dr. Alexei Khalizov Departments of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 From chemistry-request@server.ccl.net Mon Feb 14 13:11:54 2000 Received: from cornelius.INS.CWRU.Edu (root@cornelius.INS.CWRU.Edu [129.22.8.216]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA14685 for ; Mon, 14 Feb 2000 13:11:54 -0500 Received: from eje (chem51439.CHEM.CWRU.Edu [129.22.200.239]) by cornelius.INS.CWRU.Edu with SMTP (8.8.8+cwru/CWRU-3.6) id MAA11640; Mon, 14 Feb 2000 12:07:13 -0500 (EST) (from hxt10@po.cwru.edu for ) Message-ID: <000a01bf770e$0da30c20$efc81681@cwru.edu> From: "Hui-Hsu Tsai" To: Subject: Mopac subroutines Date: Mon, 14 Feb 2000 12:08:02 -0500 Dear Netters: I try to use part of Mopac subroutines, but it seems there is no detail = description about the variables and common blocks they used in the = program. Is there anyone who has experience in using the Mopac = subroutines? any help or advice is welcomed. Thanks Gavin From chemistry-request@server.ccl.net Mon Feb 14 20:30:37 2000 Received: from smaug.wrq.com (smaug.wrq.com [150.215.17.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17031 for ; Mon, 14 Feb 2000 20:30:36 -0500 Received: from abra.wrq.com (abra.wrq.com [150.215.8.10]) by smaug.wrq.com (8.8.6 (PHNE_17135)/8.8.6) with ESMTP id QAA28010 for ; Mon, 14 Feb 2000 16:25:50 -0800 (PST) Received: by abra.wrq.com with Internet Mail Service (5.5.2448.0) id ; Mon, 14 Feb 2000 16:25:50 -0800 Message-ID: <86EDBD151558D311BB5700508B2E03FC01E47B03@pikachu.wrq.com> From: Mark Thompson To: "'chemistry@ccl.net'" Subject: Message software on Linux ? Date: Mon, 14 Feb 2000 16:25:41 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Is there any messaging software available on Linux that is free or very low cost? Specifically, I'm looking for something that implements Sun's Java Messaging System API (JMS). There are lots of commercial implementations, but they are very expensive enterprise-type packages. I'm also interested in any C++ based messaging systems as well. Also, of interest would be the ability to run an Windows NT machine at one end of the pipe and a Linux box at the other. In this case, the NT machine will be running a UI app and launching computations on remote Linux boxes. Thanks for any info. I'll summarize interesting responses. Mark Thompson Seattle