From chemistry-request@server.ccl.net Wed Aug 30 03:02:36 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA24543 for ; Wed, 30 Aug 2000 03:02:36 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id JAA39820 for ; Wed, 30 Aug 2000 09:02:28 +0200 (MET DST) Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <39ABB2FE.CA7047CD@guomai.sh.cn> References: <39ABB2FE.CA7047CD@guomai.sh.cn> Date: Wed, 30 Aug 2000 09:06:00 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:Is the scale available for B3LYP/LanL2DZ FREQ calculation? Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Hi, everyone, > >I tried some metal clusters' G98 jobs in these days. I cannot find the >frequency scales for LanL2DZ basis set. Could somebody have the scale >for B3LYP/LanL2DZ? If possible, please tell me the reference. For once and for all. The scaling factors are from ancient history when it was known that RHF gave rather bad (i.e. low) frequency values. Some people used scaling factors to (ad hoc) increase these values, but these factors should be treated with special care. Since they are averaged over some set of molecules, it doesn't necessarily mean that the molecule you are treating right now exhibits the error in the same amount. This is especially true for DFT calculations which normally give very good agreement with experimental frequencies. In my opinion these factors should be ignored all over. Therefore the answer is: it is one (1.0000). M. Swart From chemistry-request@server.ccl.net Wed Aug 30 07:44:29 2000 Received: from fyserv1.fy.chalmers.se (fyserv1.fy.chalmers.se [129.16.110.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA26607 for ; Wed, 30 Aug 2000 07:44:28 -0400 Received: from fy.chalmers.se (ftf-pc33.fy.chalmers.se [129.16.112.163]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id NAA28562; Wed, 30 Aug 2000 13:44:58 +0200 (MET DST) Message-ID: <39841724.6C54EAB8@fy.chalmers.se> Date: Sun, 30 Jul 2000 13:53:08 +0200 From: Patrik Johansson X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:Is the scale available for B3LYP/LanL2DZ FREQ calculation? References: <39ABB2FE.CA7047CD@guomai.sh.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Well, I do strongly disagree with the opinion expressed by Marcel Swart. Still, RHF calculations are the only methods practically useful for large molecules and therefore these ancient(?) scaling factors to _lower_ the to _high_ frequencies obtained are most useful. I wouldn't call a paper like Scott & Radom JPC 1996 an ancient one... And, of course no one uses _anything_ without verifying that it actually works - that is, gives a good comparison with experiment. And if we go back to the original question - I've used the scaling factors for HF/6-31G* (0.89) for calculations with HF/LanL2DZ on Ag and the rest of the molecule just HF/6-31G* and it worked fine against my experimental Raman data. Therefore you could try the B3LYP/6-31G* one - should be 0.98 or better - I don't remember right now. Patrik Marcel Swart wrote: > > >Hi, everyone, > > > >I tried some metal clusters' G98 jobs in these days. I cannot find the > >frequency scales for LanL2DZ basis set. Could somebody have the scale > >for B3LYP/LanL2DZ? If possible, please tell me the reference. > > For once and for all. > > The scaling factors are from ancient history when it was known that > RHF gave rather bad (i.e. low) frequency values. Some people used > scaling factors to (ad hoc) increase these values, but these factors > should be treated with special care. Since they are averaged over > some set of molecules, it doesn't necessarily mean that the molecule > you are treating right now exhibits the error in the same amount. > This is especially true for DFT calculations which normally give very > good agreement with experimental frequencies. > > In my opinion these factors should be ignored all over. > > Therefore the answer is: it is one (1.0000). > > M. Swart > > -= 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 Wed Aug 30 09:57:51 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA27107 for ; Wed, 30 Aug 2000 09:57:50 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id PAA19390 for ; Wed, 30 Aug 2000 15:57:38 +0200 (MET DST) Date: Wed, 30 Aug 2000 15:57:38 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: independent MEP / IRC code Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, is there a freely available program doing MEP/IRC (intrinsic reaction coordinate), which I could interface with a SCF engine of my choice, e.g. Turbomole? (I do not have access to G94/98) Any pointer is highly appreciated. Regards, Peter --------------------------------------------------------------------------- Peter Burger Anorg.-chem. Institut University of Zuerich chburger@aci.unizh.ch From chemistry-request@server.ccl.net Wed Aug 30 02:26:26 2000 Received: from ns.jnj.be (dns1.be.jnj.com [194.74.108.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA24389 for ; Wed, 30 Aug 2000 02:26:25 -0400 Received: from smtp.jnj.com by smtp.jnj.com id IAA24308; Wed, 30 Aug 2000 08:26:18 +0200 (MET DST) Received: FROM ncsbebeexh3.ncsbe.jnj.com BY ncsbebesvc06.jnjeu.jnj.com ; Wed Aug 30 08:26:17 2000 +0200 Received: by ncsbebeexh3.ncsbe.jnj.com with Internet Mail Service (5.5.2651.58) id ; Wed, 30 Aug 2000 08:26:17 +0200 Message-ID: <63575A10E3FAD1119DDC0008C7242D3E032DF293@JANBEBEEXS3.janbe.jnj.com> From: "Kuppens, Tom [JanBe Extern]" To: "'CCL'" Subject: NMR literature Date: Wed, 30 Aug 2000 08:26:15 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2651.58) Content-Type: text/plain; charset="iso-8859-1" Hi all, I'm starting a project on NMR ab-initio calculations. Does someone have an idea of a good starting point in the literature ? regards Tom Kuppens University Ghent tom@hartree4.rug.ac.be From chemistry-request@server.ccl.net Wed Aug 30 05:26:40 2000 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.136.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA25276 for ; Wed, 30 Aug 2000 05:26:39 -0400 Received: from chmibm275 (chmibm275.leeds.ac.uk [129.11.137.177]) by chemistry.leeds.ac.uk (8.9.0/8.9.0) with SMTP id KAA28721; Wed, 30 Aug 2000 10:26:29 +0100 (BST) Message-Id: <3.0.6.32.20000830102812.007d6100@chmsun1.leeds.ac.uk> X-Sender: wolfgang@chmsun1.leeds.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 30 Aug 2000 10:28:12 +0100 To: Marcel Swart From: Wolfgang Roth Subject: Re: about scaling factors... Cc: CHEMISTRY@ccl.net In-Reply-To: References: <39ABB2FE.CA7047CD@guomai.sh.cn> <39ABB2FE.CA7047CD@guomai.sh.cn> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, >For once and for all. > >The scaling factors are from ancient history when it was known that >RHF gave rather bad (i.e. low) frequency values. Some people used >scaling factors to (ad hoc) increase these values, but these factors >should be treated with special care. Since they are averaged over >some set of molecules, it doesn't necessarily mean that the molecule >you are treating right now exhibits the error in the same amount. I completely agree with that Marcel, but, >This is especially true for DFT calculations which normally give very >good agreement with experimental frequencies. This statement is useless without any given proof. The ratio between experimental and theoretical/calculated frequencies may be closer to one than for HF calculations but this depends on the chosen functional and basis set... >In my opinion these factors should be ignored all over. I agree to a certain point: To interpret a vibrational or vibronic spectrum it is very useful to work with scaling factors to assign all the signals. Tabulated values might provide a useful hint to start with. But I do not believe that a scaling factor obtained from a fit to the G2 set of molecules will be a reliable estimation for metallo-organic compounds. To me, the ratio of experimental and calculated vibrational frequencies is a good measure to evaluate theoretical methods: For MP2/6-311G(d,p) and a number of aromatic molecules, the ration for the modes below 2000 cm^-1 is about 1 while it is 0.95 for the x-H stretch vibration above 3000 cm^-1. The overall "scaling" factor would be around 0.99 but the deviation between exp. and calc. for the latter modes makes the assignment difficult in some cases. However, at this level of theory Wilsons/Varsanyis mode 4 turns out to be completely wrong... Your assumption of a scaling factors with is one for all cases implies that theory is -at least- more exact or reliable that the experimental spectrum. >Therefore the answer is: it is one (1.0000). Adding decimals to the cipher/numeral does not increase the 'correctness' of that value... Regards Wolfgang Roth ==W=R==========================W=o=l=f=g=a=n=g==R=o=t=h== University of Leeds School of Chemistry Leeds LS2 9JT UK ========== http://home.germany.net/100-500777/ ========== From chemistry-request@server.ccl.net Wed Aug 30 09:57:36 2000 Received: from email.guomai.sh.cn (alhogxrywa@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA27098 for ; Wed, 30 Aug 2000 09:57:33 -0400 Received: from guomai.sh.cn ([202.101.33.151]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0G0300J4QZEMKH@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Wed, 30 Aug 2000 22:11:11 +0800 (CST) Date: Wed, 30 Aug 2000 21:49:52 +0800 From: Yubo Fan Subject: Re:ECP for Lanthanides To: CHEMISTRY@ccl.net Message-id: <39AD1100.E4F30E49@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, > > I am going to deal with some reaction concerning Lanthanides. And I > found a reference (M. Kaupp, P.v.R. Schleyer, M. Dolg, H. Stoll, J. Am. > Chem. Soc. 1992, 114, 8202), in which some particular ECP basis sets > were used. These ECPs treat [Kr]_4d10_4fx as fixed core. Could you > please tell me where can I get these basis sets. If I muse edit the G98 > files for these basis sets based on references, how should I do. > > I will summarize. > > Thanks in advance > > Y. Fan Hi, Thanks for all reply messages. I have got types of answers. 1. Download from http://www.emsl.pnl.gov:2080/forms/basisform.html I had tried several times before I sent a message to CCL, but Lanthanides seem not to be supported. I tried "Samarium" and this basisform told me the 62 element was not supported. 2. SDD basis set in G98 I tried B3LYP/SDD calculation on Samrium-containing molecules. Unfortunately, 4d and 4f electrons are included in calculation. 4f orbitals of Lanthanides are not involved signicantly in lanthanide-ligand bonds. Namely, 4f orbitals can be ignored in calculations. -- ============================================================= 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 Wed Aug 30 12:09:07 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA28134 for ; Wed, 30 Aug 2000 12:09:06 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id LAA08153 for ; Wed, 30 Aug 2000 11:08:51 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id LAA29282 for ; Wed, 30 Aug 2000 11:08:50 -0500 (CDT) Date: Wed, 30 Aug 2000 11:08:49 -0500 (CDT) From: TREVOR D POWER To: chemistry@ccl.net Subject: Re: CCL:NMR literature In-Reply-To: <63575A10E3FAD1119DDC0008C7242D3E032DF293@JANBEBEEXS3.janbe.jnj.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tom, For sure, this is not my area of research. However, one of the "big shots" in theoretical chemistry and NMR chemical shifts is Prof. Chesnut (not Chestnut) at Duke University. I am sure there are a great many others but perhaps this will allow you to begin collecting papers. Regards, Trevor D. Power Department of Chemistry NT Station, Box 305070 University of North Texas Denton, TX 76203-5070 tdp0006@unt.edu On Wed, 30 Aug 2000, Kuppens, Tom [JanBe Extern] wrote: > Hi all, > > I'm starting a project on NMR ab-initio calculations. > Does someone have an idea of a good starting point in the literature ? > > > regards > > Tom Kuppens > > > University Ghent > tom@hartree4.rug.ac.be > > > -= 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 Wed Aug 30 11:13:04 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27816 for ; Wed, 30 Aug 2000 11:09:42 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id OAA11320 for ; Wed, 30 Aug 2000 14:36:14 +0200 Date: Wed, 30 Aug 2000 14:36:14 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: Linux settings to run in parallel Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I have been trying to run in parallel in a Pentium dual with Linux (Red Hat), with little success. Are there any settings (in the lilo.conf or somewhere else) to specify that a job can be sent to both processors ? Thanks a lot. Damian Scherlis Department of Chemical Physics Faculty of Sciences University of Buenos Aires. From chemistry-request@server.ccl.net Wed Aug 30 15:33:37 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29057 for ; Wed, 30 Aug 2000 15:33:37 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id OAA18179; Wed, 30 Aug 2000 14:32:57 -0500 (EST) Message-ID: Date: 30 Aug 2000 14:48:57 -0500 From: "Boyd" Subject: re: NMR shielding To: "Kuppens, Tom" Cc: "OSC CCL" , "Power, Trevor D." X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi, To answer Tom Kuppens' question about where to start in the literature and following up on Trevor D. Power's suggestion to see the work of Donald Chesnut, you may wish to read: D. B. Chesnut, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 8, pp. 245-297. The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Aug 30 15:07:35 2000 Received: from lrz.uni-muenchen.de (root@A4091.pppool.de [213.6.64.145]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA28963 for ; Wed, 30 Aug 2000 15:07:30 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id KAA06331; Wed, 30 Aug 2000 10:17:34 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14765.16814.629771.63211@lrz.uni-muenchen.de> Date: Wed, 30 Aug 2000 10:17:34 -0700 (PDT) To: Subject: New York City meeting for the Chemical Information Community featuring Bill Town X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid From: "Slutsky, Bruce" Sender: CHEMICAL INFORMATION SOURCES DISCUSSION LIST To: CHMINF-L@LISTSERV.INDIANA.EDU Subject: New York City meeting for the Chemical Information Community featuring Bill Town Date: Wed, 30 Aug 2000 13:57:24 -0400 The Computers in Chemistry Topical Group of the New York Section is pleased to announced that CINF's Bill Town will be speaking on: Chemical Communities on the Web: Success Factors New York University Department of Chemistry Main Building Room 1003 31 Washington Place New York, NY Wednesday September 27, 2000 Dinner 4:00 PM (cost will be approximately $20) Social Hour 5:30 PM Seminar 6:00 PM (no charge to attend just the seminar) For further information contact Bruce Slutsky (contact information below) or John Halpin at 212-998-8418 john.halpin@nyu.edu Please contact John Halpin if you want to go to dinner. He will need to know the number of people attending Bruce Slutsky New Jersey Institute of Technology Robert Van Houten Library 323 Martin Luther King Blvd Newark, NJ 07102-1982 voice 973-642-4950 fax 973-643-5601 e-mail Bruce.Slutsky@njit.edu From chemistry-request@server.ccl.net Wed Aug 30 16:31:55 2000 Received: from nets5.rz.rwth-aachen.de (nets5.rz.RWTH-Aachen.DE [137.226.144.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29327 for ; Wed, 30 Aug 2000 16:31:54 -0400 Received: from zosia (zosia.dorf.RWTH-Aachen.DE [134.130.59.212]) by nets5.rz.rwth-aachen.de (8.10.1/8.10.1/5) with SMTP id e7UKUpM15154; Wed, 30 Aug 2000 22:30:52 +0200 (MET DST) Message-ID: <000901c012c1$92d514c0$d43b8286@dorf.rwthaachen.de> From: "Krzysztof Radacki" To: =?iso-8859-1?Q?Dami=E1n_Scherlis?= Cc: References: Subject: Re: CCL:Linux settings to run in parallel Date: Wed, 30 Aug 2000 22:33:34 +0200 Organization: AC RWTH Aachen MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Hi, LILO ? Strange place to look for - its just boot-loader. Or maybe you mean starting a smp-kernel - normaly redhat should setup smp if you have two processors. If not, then with tab-key you can see all of kernels available in your /boot. What you surely need is setting value in shmmax file (on redhat-systems /proc/sys/kernel/shmmax) on ca. 80% of your memory. This is shared mammory for smp. Without changing its value you can start jobs only with ca. 35MB per processor. The next question is what program you're useing. For example in gaussian-input you have to add #NPROC=2 line somewhere on the begining of input-file. MfG Krzys ----- Original Message ----- From: "Damián Scherlis" To: Sent: Wednesday, August 30, 2000 2:36 PM Subject: CCL:Linux settings to run in parallel > > Hello, > > I have been trying to run in parallel in a Pentium dual > with Linux (Red Hat), with little success. Are there any > settings (in the lilo.conf or somewhere else) > to specify that a job can be sent to both processors ? > > Thanks a lot. > > > Damian Scherlis > Department of Chemical Physics > Faculty of Sciences > University of Buenos Aires. > > > > -= 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 > > > > > >