From chemistry-request@server.ccl.net Wed Apr 26 00:52:44 2000 Received: from exconnect.levels.unisa.edu.au (exconnect.levels.unisa.edu.au [130.220.36.204]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA08521 for ; Wed, 26 Apr 2000 00:52:42 -0400 Received: by exconnect.levels.unisa.edu.au with Internet Mail Service (5.5.2232.9) id ; Wed, 26 Apr 2000 14:22:33 +0930 Message-ID: <5DA42F8A3C18D111979400AA00DD609D021E9411@exstaff3.levels.unisa.edu.au> From: Andrea Gerson To: "'chemistry@ccl.net'" Subject: Examples for simple lecture on all types of molecular modelling Date: Wed, 26 Apr 2000 14:22:30 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Dear All, I have been asked to do a simple one hour lecture in which I should cover the basics of molecular modelling. By the basics I do not mean the theory just which types of theory (atomistic potential, semi-empirical, ab initio etc...) are useful for what kind of applications. Because the people I will be talking to are not modellers it would be nice to have some colourful examples and simulations (dynamics) to liven up the lecture a bit. If anybody has this kind of thing on hand (anything from solid state band structures to protein conformation to dynmaic simulations) it would be most appreciated it if you could e-mail it to me or point me in the direction of a web site. Thanks very much Andrea From chemistry-request@server.ccl.net Wed Apr 26 11:14:55 2000 Received: from maile.surrey.ac.uk (maile.surrey.ac.uk [131.227.102.10]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA11869 for ; Wed, 26 Apr 2000 11:14:54 -0400 Received: from lt-ces1mb (actually host ip192.cpe.surrey.ac.uk) by maile.surrey.ac.uk with SMTP Local (PP); Wed, 26 Apr 2000 16:13:43 +0100 Message-Id: <3.0.5.32.20000426161542.008114a0@pop.surrey.ac.uk> X-Sender: ces1mb@pop.surrey.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 26 Apr 2000 16:15:42 +0100 To: chemistry@ccl.net From: Dr Mark J Biggs Subject: QM study of heterogeneous reactions Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi All! I have a question relating to QM study of reactions relevent to heterogeneous catalysis. I have never done such simulations before, but have a number of papers which report such work. One of the papers (Schneider et al., J. Phys. Chem. B, V101, p4353, 1997) I have seeks to determine the mechanism for NO decomposition over Cu-ZSM5. This paper indicates that the --Cu .. O-N configuration (i.e. oxygen down) is the lowest energy configuration. From this start point, a mechanism is then determined. However, they also say that the --Cu .. N-O configuration is only slightly more energetic than the O-down configuration. My question is: Why should we pick any one particular starting configuration? Let me outline my motivation for this question so that I do not get the obvious answer (i.e. minimum energy configuration as revealed by QM sim on model used)! The models used in QM are normally small cluster models which cannot take into account the steric effects imposed by cages or other fluid molecules. It is possible that the solid structure and other fluid molecules may make it difficult to acheive an O-down configuration as simulated above. Even if the cluster is adequate, there is likely to be various angles of approach and orientations of the molecule relative to the Cu site at typical reaction temperatures, and the molecule may not ever have time to "get itself" into the O-down position before a second NO arrives and a reaction possibly occurs. The reaction configuration may, therefore, never be able to start from the initial configuration assumed on the basis of minimum energy as determined by the cluster model, and may never follow the path of minimum PE. Whilst I have used the above paper as an example, it appears as if this approach is used in all papers I have (even so-called "dynamic QM" using DFT MD). Answers can be sent to m.biggs@surrey.ac.uk Many thanks in advance. Mark Biggs From chemistry-request@server.ccl.net Wed Apr 26 11:44:29 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12024 for ; Wed, 26 Apr 2000 11:44:28 -0400 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id RAA21216; Wed, 26 Apr 2000 17:44:12 +0200 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id RAA10657; Wed, 26 Apr 2000 17:44:09 +0200 Date: Wed, 26 Apr 2000 17:44:07 +0200 (MDT) From: Harald Svedung To: elewars cc: chemistry@ccl.net Subject: Re: CCL:van der Waals SURFACES/ELECTRON DEN In-Reply-To: <39061DAA.E9D88A8D@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would just like to make a small comment on the side: The van der Waals size applies to a very simple picture of a molecular system. It is quite useful in many cases but (and this is my perhaps misdirected warning) when it comes to scattering processes, e.g. collisional energy transfer, the shape of the repulsive wall is of course important. How to go from electron density to the correct repulsive potential is discussed in e.g.: C. Nyeland, J. P. Toennies, Chem. Phys. 188 (1994) 205. There is also work in progress in this field. yours :-) The spring has finally come here in Goeteborg! Harald On Tue, 25 Apr 2000, elewars wrote: > 2000 April 25 > > Hello, > > I once read somewhere that an isosurface that encloses 97% of the total > electron density of a molecule corresponds best to the experimental van > der Waals surface. > > (1) Has anyone a reference to this, or to any percentage of the electron > density? > (2) Is it correct to say that the usual way to measure the "van der > Waals size" of a molecule is by X-ray diffraction (the molecules in a > crystal being considered to be in contact)? > > Thanks. > > E. Lewars > ======> > Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Tue Apr 25 18:29:46 2000 Received: from hotmail.com (law-f112.hotmail.com [209.185.131.175]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA06848 for ; Tue, 25 Apr 2000 18:29:46 -0400 Received: (qmail 18348 invoked by uid 0); 25 Apr 2000 22:27:44 -0000 Message-ID: <20000425222744.18347.qmail@hotmail.com> Received: from 205.247.153.213 by www.hotmail.com with HTTP; Tue, 25 Apr 2000 15:27:44 PDT X-Originating-IP: [205.247.153.213] From: "govindan subramanian" To: chemistry@ccl.net Subject: non-linear regressions Date: Tue, 25 Apr 2000 15:27:44 PDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Dear CCL'ers I am interested in knowing about any freeware/shareware for performing non-linear regressions in UNIX/Windows platform. My immediate interest is to perform sigmoidal fitting. Any possible indicators are welcome. Will summarize if there is sufficient interest. Thanks. -subramanian.g ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Tue Apr 25 19:30:35 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA07178 for ; Tue, 25 Apr 2000 19:30:34 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id QAA11505; Tue, 25 Apr 2000 16:29:33 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14598.10841.937841.764382@lrz.uni-muenchen.de> Date: Tue, 25 Apr 2000 16:29:29 -0700 (PDT) To: Subject: [BioPython] biocorba progress X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid From: Ewan Birney Sender: biopython-admin@biopython.org To: biopython@biopython.org, biojava-l@biojava.org, bioxml-dev@bioxml.org Subject: [BioPython] biocorba progress Date: Tue, 25 Apr 2000 20:59:26 +0100 (BST) [excuse the cross post] Just popping over from bioperl. Just to say that bioperl biocorba server implementation is ticking along nicely. For the biojava and biopython project I'd encourage you to look at developing clients to these objects - this way you can bootstrap off the 'maturity' (aka - cruft) of bioperl, giving you access to sequence flat files and sequence databases automatically without going nuts over the quirks of sequence formats. read: http://www.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl/0004/0027.html I cc'd bioxml in so they didn't feel sidelined - xml and corba are pretty orthogonal technologies, and both have their place. bioxml will play naturally with biocorba once it gets into bioperl. In other words, writing bioxml parsers in bioperl and then letting this functionality be exported via biocorba will give a way of getting XML parsing to all 3 projects at the same time. This will happen without anyone in bioxml needing to understand the biocorba stuff... (whey hey!) Thanks for listening to this transmission... ewan ----------------------------------------------------------------- Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420 . ----------------------------------------------------------------- _______________________________________________ BioPython mailing list - BioPython@biopython.org http://biopython.org/mailman/listinfo/biopython From chemistry-request@server.ccl.net Tue Apr 25 23:43:03 2000 Received: from hotmail.com (oe13.law3.hotmail.com [209.185.240.117]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA08287 for ; Tue, 25 Apr 2000 23:43:02 -0400 Received: (qmail 89731 invoked by uid 65534); 26 Apr 2000 03:40:57 -0000 Message-ID: <20000426034057.89730.qmail@hotmail.com> X-Originating-IP: [161.142.78.83] From: "Yeoh Hak Koon" To: "CCL" Subject: HOMO-LUMO vs. lambda max Date: Wed, 26 Apr 2000 11:35:54 +0800 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 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Colleagues, Something not addressed in all past postings : What are the reservations or objections of equating the HOMO-LUMO energy gap to the maximum wavelength peak (lambda max) in a UV-Vis spectra? Are these the reasons? (a) the HOMO-LUMO transition might be forbidden, hence does not show up in the spectra (b) the lambda max has vibrational contributions, so it is usually more energetic than the 0-0 transition predicted. For (a), is there a way to predict whether the transition is forbidden or not? (I am using a commercial software PC Spartan Pro). For (b), since at room temperature, the vibrational energy is relatively small, I could still say the approximation is acceptable, right? My apologies if these insult your intelligence; I am not trained as a chemist, but a chemical engineer. Thank you very much. Best regards, H. K. Yeoh 26 April 2000 From chemistry-request@server.ccl.net Wed Apr 26 11:58:17 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 LAA12124 for ; Wed, 26 Apr 2000 11:58:16 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA26190 for ; Wed, 26 Apr 2000 08:55:53 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost via smap (V2.0) id xma026182; Wed, 26 Apr 00 08:55:48 -0700 Message-Id: <4.3.0.20000426083022.00b0f610@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Wed, 26 Apr 2000 08:31:16 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Workshops in York, UK Molecular Simulations Inc. will be holding a pair of workshops 19-23 June 2000 at the University of York, York, UK. These workshops are relevant to any of our customers who are novices to the Cerius2 interface and who are interested in combinatorial chemistry applications. From 19-20 June, the <> will be conducted. This is the introductory workshop to acquaint new users to the Cerius2 user interface. Basic operations with the interface will be the main focus of the workshop but commonly used modules will also be discussed. Attendees should possess knowledge of basic UNIX commands and a basic understanding of molecular modeling. No prior experience with Cerius2 is required. The second workshop will be held from 21-23 June. This three-day workshop, <>, will cover basic aspects of quantitative structure-activity relationships (QSAR) and combinatorial library design, from initial library specification through library analysis techniques. The Cerius2 interface will be used throughout the workshop. Fees for the two-day <> are GBP 630 commercial, GBP 315 government, and GBP 250 academic. Fees for the three-day <> are GBP 945 commercial, GBP 475 government, and GBP 375 academic. Register for both classes and receive a 25% discount on the total amount. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website ( http://www.msi.com/about/events/training ). Please do not hesitate to contact me should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Training Programs 011- 58-799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Wed Apr 26 14:29:20 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA13306 for ; Wed, 26 Apr 2000 14:29:19 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id UAA03684; Wed, 26 Apr 2000 20:29:42 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14599.13717.169934.242262@yogi.pc1.uni-duesseldorf.de> Date: Wed, 26 Apr 2000 20:29:41 +0200 (CEST) From: Jochen Kuepper To: govindan subramanian Cc: chemistry@ccl.net Subject: CCL:non-linear regressions In-Reply-To: <20000425222744.18347.qmail@hotmail.com> References: <20000425222744.18347.qmail@hotmail.com> X-Mailer: VM 6.72 under 21.1 (patch 9) "Canyonlands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA13307 >>>>> "govindan" == govindan subramanian writes: > Dear CCL'ers I am interested in knowing about any > freeware/shareware for performing non-linear regressions in > UNIX/Windows platform. My immediate interest is to perform > sigmoidal fitting. Any possible indicators are welcome. Will > summarize if there is sufficient interest. Thanks. www.netlib.org Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.Jochen-Kuepper.de From chemistry-request@server.ccl.net Wed Apr 26 14:42:25 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA13460 for ; Wed, 26 Apr 2000 14:42:25 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA28833; Wed, 26 Apr 2000 14:42:20 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <390739B5.4EB99ADA@syr.edu> Date: Wed, 26 Apr 2000 14:47:17 -0400 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Yeoh Hak Koon CC: CCL Subject: Re: CCL:HOMO-LUMO vs. lambda max References: <20000426034057.89730.qmail@hotmail.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A simple HOMO-LUMO approach to calculating lambda max is fundamentally incorrect. Spectroscopic properties require a good knowledge of the excited state surface, which ground state geometry optimization methods, like HF, will not give you. For an excitation to be visible, (i) it must be allowed, (ii) it should not have an oscillator strength close to 0. To calculate abosrption maxima one has to apply some method which includes electron correlation and can be applied to excited states The easiest way to calculate absorption maxima is to use a CI method like ZINDO. Of course, ZINDO fails in cases like polyenes which have low lying forbidden states, but it is a start. Deepak. Yeoh Hak Koon wrote: > Dear Colleagues, > > Something not addressed in all past postings : > > What are the reservations or objections of equating the HOMO-LUMO energy gap > to the maximum wavelength peak (lambda max) in a UV-Vis spectra? > > Are these the reasons? > (a) the HOMO-LUMO transition might be forbidden, hence does not show up in > the spectra > (b) the lambda max has vibrational contributions, so it is usually more > energetic than the 0-0 transition predicted. > > For (a), is there a way to predict whether the transition is forbidden or > not? (I am using a commercial software PC Spartan Pro). > > For (b), since at room temperature, the vibrational energy is relatively > small, I could still say the approximation is acceptable, right? > > My apologies if these insult your intelligence; I am not trained as a > chemist, but a chemical engineer. Thank you very much. > > Best regards, > H. K. Yeoh > 26 April 2000 > > -= 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 -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin **********************************************************************