From chemistry-request@server.ccl.net Wed Jun 5 04:38:34 2002 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g558cXF06598 for ; Wed, 5 Jun 2002 04:38:33 -0400 Received: from b159504364 (PPP169.fukuoka-ip.dti.ne.jp [211.132.92.169]) by smtp1.dti.ne.jp (3.07) with SMTP id g558cPmg005570 for ; Wed, 5 Jun 2002 17:38:28 +0900 (JST) Message-ID: <002f01c20c6c$6ca43fa0$a95c84d3@b159504364> From: "Telkuni" To: Subject: Suitable system for EHMO Date: Wed, 5 Jun 2002 17:38:53 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Suitable system for EHMO Hello CCLers, I have read the explanation of Extended Huckel MO(EHMO) method on one book (Sorry, it is Japanese!) It said "EHMO isn't SCF, so it isn't available for the systems which have the polarizability, especially not for the polypeptides. " But, I saw some examples of other articles on which EHMO have been applied to polar-systems. So I like to know the systems which are suitable or not-suitable for EHMO. I will summarize the responses. Thanks in advance. ------------------------------------------------ Telkuni Tsuru Kyushyu Electronic Technology and Research telkuni@venus.dti.ne.jp ------------------------------------------------ From chemistry-request@server.ccl.net Wed Jun 5 06:00:07 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55A07F08403 for ; Wed, 5 Jun 2002 06:00:07 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 620532DCC55; Wed, 5 Jun 2002 12:00:06 +0200 (CEST) Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id 951212DCC52; Wed, 5 Jun 2002 12:00:05 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA04752; Wed, 5 Jun 2002 11:27:25 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 5 Jun 02 12:00:05 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 5 Jun 02 11:59:58 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Peter Waaben Thulstrup Date: Wed, 5 Jun 2002 11:59:52 +0100 Subject: Re: CCL:G98 TD/CIS Opposite sign of the components of length- a Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <2F8E25479E6@virgil.ruc.dk> Hello Peter: > I have some questions regarding the output os CIS and TD jobs in G98 > (Rev. A7). I can't find anything on these issues in Gaussian > documentation or past CCL posts, although the questions are rather > simple. So I hope it makes sense... > > The output of TD and CIS calculations give the x, y, and z > components of the "Ground to excited state Transition electric > dipole moments", "Ground to excited state transition velocity dipole > Moments", and the "Ground to excited state transition magnetic > dipole Moments". > > 1) Why are the components of the electric and velocity derived > transition dipole moments oppositely signed? I thought that they > should be identical in a complete basis. I would have thought that > the sign ought to be the same. Which values should I trust? The dipole length and dipole velocity "transition moments" are not identical. But the dipole length and dipole velocity forms of the oscillator strength, f(L) and f(V), should lead to identical results for exact wavefunctions (a.u.): f(L) = (2/3) ||^2 (Ej - Ei) f(V) = (2/3) ||^2 / (Ej - Ei) Here r is the position vector and p the momentum operator. For approximate wavefunctions, f(L) and f(V) are no longer identical, but for calculational models of high quality the two values should be close. > 2) Is it possible to say which of the computed oscillator strengths > (dipole-length or dipole-velocity derived) provide the best estimate > of experimental absorption intensities? One value is not necessarily better than the other, but usually the value derived by the dipole length expression is quoted. But as long as the two values are close, you shouldn't worry! > 3) I suppose that the computed electric and magnetic dipole moments > are origin dependent. But are the magnetic transition dipole moments > derived in a manner which make them related in to the transition > velocity dipole moments, rather than the transition electric dipole > moments? (e.g. in terms of origin dependence etc.) The electric dipole moment should NOT be origin dependent, but the magnetic dipole moment is. Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Jun 5 06:06:35 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55A6YF08602 for ; Wed, 5 Jun 2002 06:06:34 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id AE7812DCC82; Wed, 5 Jun 2002 12:06:33 +0200 (CEST) Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id CAD4F2DCC7F; Wed, 5 Jun 2002 12:06:32 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA07292; Wed, 5 Jun 2002 11:33:52 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 5 Jun 02 12:06:33 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 5 Jun 02 12:06:23 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Coussens, Betty" Date: Wed, 5 Jun 2002 12:06:21 +0100 Subject: Re: CCL:TDDFT in Gaussian Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <2F8FDC25E69@virgil.ruc.dk> Dear Betty, there is a bug in early releases of Gaussian98, leading to the prediction of much too low oscillator strengths in TD-DFT calculations. Get hold of Revision A.7 or later versions where this error has been corrected. Yours, Jens >--< > I have been using Gaussian98 Revision A.5 for performing a number of > TDDFT calculations on norbornane and norbornane like systems. As I > was performing this type of computations for the first time I tried > reproducing the spectra presented in a recent paper by Ando et al. > (Jpn. J. Appl. Phys. Vol 41 (2002) pp. L105-L108). Unfortunately, I > was not able to do so. As I had no idea why, I contacted the > authors of this paper. They were so kind to send me the output of > the TDDFT computation on norbornane they performed themselves. > Comparing their results with mine, it appeared that although the > excitation energies were similar, the oscillator strengths were > totally different. The only difference between mine and their > calculation is that I was using symmetry whereas they were not. I > had the plan to use their optimized norbornane structure and perform > exactly the same calculation as they did. However, in the meantime, > I checked the CCL for messages on TDDFT. Based on these messages, > it seems that I have to conclude that the computation of oscillator > strenghts was originally not correctly implemented in Gaussian. As > I am using Revision A.5 whereas Ando et al. have been using revision > A.9 this could probably also explain why I am not able to reproduce > the results of the Ando group. Can anybody comment on this? NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Jun 5 06:21:02 2002 Received: from netc-1v.grolier.fr ([194.158.97.217]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55AL1F08967 for ; Wed, 5 Jun 2002 06:21:01 -0400 Received: from netcourrier.com (localhost [127.0.0.1]) by netc-1v.grolier.fr (8.9.3+Sun/8.9.3) with SMTP id MAA24112; Wed, 5 Jun 2002 12:20:58 +0200 (CEST) Date: Wed, 5 Jun 2002 12:20:58 +0200 (CEST) From: eric.vangrevelinghe@netcourrier.com Received: from [194.191.169.70] by netcourrier-1v.netcourrier.com via html interface; To: jianquan@eden.rutgers.edu Cc: chemistry@ccl.net Subject: Re: CCL:calculate charge using MOPAC Mime-Version: 1.0 X-Mailer: Medianet/v2.0 Message-Id: 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 g55AL2F08968 Dear Jianquan, You should take a look on the BatchMan program: http://web.univ-orleans.fr/SCIENCES/ICOA/batchman/index.html BatchMan is a FREE graphic interface to Mopac, Gamess and Babel, mainly oriented to handle a large number of structures (batch mode). With the use of one SCF step in the mopac calculation (chose optimization: none in the Mopac keywords interface), you will be able to treat easily several thousand of structures without the need to know how Mopac works. Hope that helps. Regards, Eric. ----Message d'origine---- >Date: Tue, 4 Jun 2002 12:22:37 -0400 (EDT) >De: Jianquan Chen >A: chemistry@ccl.net >Sujet: CCL:calculate charge using MOPAC > >Hi, >I need to add charge to thousands of molecules. MOPAC is free but slow and >sometimes changes the moleucular structure. I don't know how MOPAC >works. I have 2 questions. >Can I run MOPAC without optimizing the molecular >structure? >Is there any way to accelate MOPAC? I don't need very accurate charges. > >Thanks a lot for any response. > > >Jianquan Chen > > > >-= 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 > > > > > > ------------------------------------------------------------- NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar... Web/Wap : www.netcourrier.com Téléphone/Fax : 08 92 69 00 21 (0,34 € TTC/min) Minitel: 3615 NETCOURRIER (0,15 € TTC/min) From chemistry-request@server.ccl.net Wed Jun 5 14:13:17 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55IDGF21030 for ; Wed, 5 Jun 2002 14:13:16 -0400 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.3/8.12.3) with ESMTP id g55IDCmd054270; Wed, 5 Jun 2002 11:13:13 -0700 Date: Wed, 5 Jun 2002 11:13:12 -0700 (PDT) From: Roy Jensen To: chemistry@ccl.net Subject: singlet-triplet crossings... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanned-By: MIMEDefang 2.11 (www dot roaringpenguin dot com slash mimedefang) All I would like to understand how states of different multiplicity are coupled together AND how to determine the probability of surface-crossing. Coupling is, I believe, a spin-orbit interaction. CASSCF can apparently optimize to a singlet-triplet crossing -- has anyone attempted this? I am aware of the work by Landau and Zener in the 1930s on surface crossing probabilities. Roy Jensen From chemistry-request@server.ccl.net Wed Jun 5 15:51:46 2002 Received: from berzerk.gpcc.itd.umich.edu (smtp@[141.211.2.162]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55JpkF23176 for ; Wed, 5 Jun 2002 15:51:46 -0400 Received: from xexex.gpcc.itd.umich.edu (xexex.gpcc.itd.umich.edu [141.211.2.217]) by berzerk.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id PAA10045 for ; Wed, 5 Jun 2002 15:51:45 -0400 (EDT) Received: from localhost (brupalf@localhost) by xexex.gpcc.itd.umich.edu (8.9.1a/5.1-client) with ESMTP id PAA23106 for ; Wed, 5 Jun 2002 15:51:45 -0400 (EDT) Precedence: first-class Date: Wed, 5 Jun 2002 15:51:45 -0400 (EDT) From: Bruce Allan Palfey X-X-Sender: brupalf@xexex.gpcc.itd.umich.edu To: CHEMISTRY@ccl.net Subject: ArgusLab output Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi I've started to calculate the absorbance spectra of a large number of organic molecules/complexes using ArgusLab (a very impressive program!). I was wondering if anyone knows of a convenient way to extract the calculated absorbance spectrum from the output (a text file) and display it graphically. What I'm after is basically a bar graph with a vertical line drawn at the wavelength of the transition having a height determined by the oscillator strength. Any suggestions? Bruce Palfey Department of Biological Chemistry University of Michigan Ann Arbor, MI 48109-0606 From chemistry-request@server.ccl.net Wed Jun 5 16:37:33 2002 Received: from server-6.tower-15.messagelabs.com ([63.210.62.243]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g55KbWF24181 for ; Wed, 5 Jun 2002 16:37:32 -0400 X-VirusChecked: Checked Received: (qmail 1056 invoked from network); 5 Jun 2002 20:37:09 -0000 Received: from smtp1.apci.com (HELO naex016w) (204.27.156.18) by server-6.tower-15.messagelabs.com with SMTP; 5 Jun 2002 20:37:09 -0000 Received: from naex015m.apci.com ([144.249.232.18]) by 144.249.122.20 with Trend Micro InterScan Messaging Security Suite for SMTP v5.01; Wed, 05 Jun 2002 16:33:55 -0400 Received: by naeb015m.apci.com with Internet Mail Service (5.5.2655.55) id ; Wed, 5 Jun 2002 16:37:09 -0400 Message-ID: From: "Peterson,Brian K." To: chemistry@ccl.net Subject: EIDE vs SCSI & backup in Linux clusters Date: Wed, 5 Jun 2002 16:37:02 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain; charset="iso-8859-1" Hello CCLers. We are specifying a Linux Cluster to use for a variety of codes including computational chemistry- both quantum and molecular simulations. I've looked at the CCL archives to see what people have said about SCSI vs EIDE drives in such a cluster and the results are a bit ambiguous. What are the current perspectives on disk solutions for Intel based Linux clusters? Are EIDE drives sufficient? Does one need to tune parameters to get good performance? Second question. What are you doing about backup of disks on your Linux clusters? Do you just move output files to another machine which is backed up? Thanks for any help, brian Dr. Brian K. Peterson Air Products and Chemicals, Inc. 7201 Hamilton Boulevard phone: 610-481-3850 Allentown, PA 18195-1501 fax: 610-706-7672 USA + From chemistry-request@server.ccl.net Wed Jun 5 17:41:06 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55Lf6F25601 for ; Wed, 5 Jun 2002 17:41:06 -0400 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g55Lf2B24555 for ; Wed, 5 Jun 2002 14:41:06 -0700 (PDT) Message-Id: <200206052141.g55Lf2B24555@mx.seanet.com> To: CHEMISTRY@ccl.net From: Mark Thompson Subject: Re: CCL:ArgusLab output Date: Wed, 5 Jun 2002 14:41:06 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 > I've started to calculate the absorbance spectra of a large number of > organic molecules/complexes using ArgusLab (a very impressive program!). > I was wondering if anyone knows of a convenient way to extract the > calculated absorbance spectrum from the output (a text file) and display > it graphically. What I'm after is basically a bar graph with a vertical > line drawn at the wavelength of the transition having a height determined > by the oscillator strength. Any suggestions? > > Bruce Palfey Bruce, Thanks for your email and good thoughts about the ArgusLab! Presently, you would have to extract the results by hand from the output or have a script do it for you. What you ask is actually an easy feature to add. We are working on the 3.1 minor release now. We can easily add a feature that writes a text file that contains comma-delimited excitation energy, wavelength, and intensity. This could be read directly into Excel and plotted. We've added it to the feature list for 3.1 Cheers, Mark ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Wed Jun 5 12:32:36 2002 Received: from mail.inha.ac.kr ([165.246.10.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55GWZF18223 for ; Wed, 5 Jun 2002 12:32:35 -0400 Received: by inha.ac.kr with Internet Mail Service (5.5.2653.19) id <2YVQ67C6>; Thu, 6 Jun 2002 01:22:55 +0900 Message-ID: <254361A45F4AD311B42900104B1343926656C9@inha.ac.kr> From: =?euc-kr?B?sejC+bDm?= To: "'chemistry@ccl.net'" Subject: G98 : Printing isodensity surface Date: Thu, 6 Jun 2002 01:22:54 +0900 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C20CAD.3EAA0300" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C20CAD.3EAA0300 Content-Type: text/plain Dear Computational Chemists: I would like to print a set of points(x,y,z coordinates) on the (molecular) surface of electron density 0.001 au of a molecule. Using this points, I want to calculate electrostatic potential on this surface. But I could not find an option to print this in the Gaussian 98 manual. Many programs are available for the graphic representation of the surface. But I need the cartesian coordinates of the surface. How can I do that? If not, do I need any other programs to generate such coordinates? Thanks in advance. Chan. ------_=_NextPart_001_01C20CAD.3EAA0300 Content-Type: text/html Content-Transfer-Encoding: quoted-printable G98 : Printing isodensity surface

Dear Computational Chemists:

    I would like to print a set of = points(x,y,z coordinates) on the (molecular) surface of electron = density 0.001 au of a molecule. Using this points, I want to calculate = electrostatic potential on this surface. But I could not find an option = to print this in the Gaussian 98 manual. Many programs are available = for the graphic representation of the surface. But I need the cartesian = coordinates of the surface.

   How can I do that? If not, do I need any = other programs to generate such coordinates?

Thanks in advance.

Chan.

------_=_NextPart_001_01C20CAD.3EAA0300-- From chemistry-request@server.ccl.net Wed Jun 5 15:33:30 2002 Received: from hisar.cc.boun.edu.tr ([193.140.192.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g55JXSF22732 for ; Wed, 5 Jun 2002 15:33:29 -0400 Received: by hisar.cc.boun.edu.tr (Postfix, from userid 4210) id 4DC48134F; Wed, 5 Jun 2002 22:31:35 +0300 (EET DST) Received: from localhost (localhost [127.0.0.1]) by hisar.cc.boun.edu.tr (Postfix) with ESMTP id 4083CFCA; Wed, 5 Jun 2002 22:31:35 +0300 (EET DST) Date: Wed, 5 Jun 2002 22:31:35 +0300 (EET DST) From: "Alimet S. Ozen" X-Sender: ozensem@hisar.cc.boun.edu.tr To: "xmao@biosino.org" Cc: "chemistry@ccl.net" Subject: Re: CCL:reactivity of a molecule In-Reply-To: <200206042258103.SM00279@mao> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g55JXUF22733 Hello, Unfortunately I don't know such a website but you can employ chemical reactivity indices such as Fukui functions, global(for intermolecular reactivity) and local(for intra-molecular reactivity or site selectivity) hardness and softness values to determine for example the most susceptible site for electrophilic,nucleophilic or radical reactions. If the energy of a system is considered as a function of number of electrons and external potential, then its reactivity is determined by its sensitivity to perturbations in these.For example in its simplest form,the change in energy wrt a change in number of electrons is the hardness, the change in electron density with a change in the number of electrons is called the fukui functions(condensed fukui functions are simply calculated > from the atomic charges)..etc.. Here are some references I can suggest you to have a look at: 1. Chermette H. "Chemical Reactivity Indexes in Density functional Theory" J. Comp.Chem,1999, 20,129-154 2. Parr R.G; Yang W. Density Functional Theory of Atoms and Molecules Oxford Univ.Press 1989 3. Geerlings P; De Proft F, Langenaker W. Advances in Quantum Chemistry, 33, 1999 4. Pearson R.G. J.Chem Ed, 1999,76,267 and there are many others... I hope it helps.. Best Regards Alimet On Tue, 4 Jun 2002, xmao@biosino.org wrote: > Hello Everyone: > I wonder if there are some tutorails on the website or some references that teach how to get the reactivity of a molecule from the quantum chemistry calculation results. > > > > Ö > Àñ£¡ > > xmao > xmao@biosino.org > > > > -= 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 > > > > > > "Real value:is not the one whose presence fills an empty space but the one whose absence creats one" Ozdemir Asaf ozensem@boun.edu.tr alimetsema@yahoo.com http://www.geocities.com/alchemistrial