From chemistry-request@server.ccl.net Wed Dec 5 01:49:07 2001 Received: from smtp6.mindspring.com ([207.69.200.110]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB56n6i09594 for ; Wed, 5 Dec 2001 01:49:07 -0500 Received: from user-1120d2m.dsl.mindspring.com ([66.32.52.86] helo=josiah) by smtp6.mindspring.com with esmtp (Exim 3.33 #1) id 16BVrU-0002Kh-00 for chemistry@ccl.net; Wed, 05 Dec 2001 01:48:56 -0500 Message-ID: <15e401c17d57$944a2b40$0301a8c0@josiah.dalkescientific.com> Reply-To: "Andrew Dalke" From: "Andrew Dalke" To: Subject: Re: CCL:FYI: [Bioinformatics] Open Source Petition FAQ (fwd) Date: Tue, 4 Dec 2001 23:39:23 -0700 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 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Eugene Leitl posted: >Subject: [Bioinformatics] Open Source Petition FAQ As a note, this is the first draft of the FAQ and was posted for comment on the Bioinformatics list hosted at O'Reilly. It was not meant to be widely distributed. The views are currently those of the FAQ author rather than of the petition signers or those involved in the discussion (like me). If you are interested in adding to the discussion, please visit the main site for the petition at http://www.openinformatics.org/ and also read the discussion archives at http://labs.oreilly.com/mailman/listinfo/bioinformatics Since my name was listed right at the top of Eugene's forward, let me also add that I am against the petition, for reasons outlined later on in the text. That description will be updated in the next version of the FAQ to better explain my position. Andrew Dalke dalke@dalkescientific.com From chemistry-request@server.ccl.net Wed Dec 5 06:20:38 2001 Received: from dire.bris.ac.uk ([137.222.10.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5BKai16963 for ; Wed, 5 Dec 2001 06:20:37 -0500 Received: from eis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Wed, 5 Dec 2001 11:20:17 +0000 Received: from localhost (localhost [127.0.0.1]) by eis.bris.ac.uk (8.11.6/8.11.6) with SMTP id fB5BImZ18232; Wed, 5 Dec 2001 11:18:48 GMT Date: Wed, 5 Dec 2001 11:18:48 +0000 (GMT) From: DE Parry To: "Konstantin N. Kudin" cc: chemistry Subject: Re: CCL:Periodic systems: Fermi level at the band crossing In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 4 Dec 2001, Konstantin N. Kudin wrote: > I am looking for examples of metallic 2D and 3D periodic systems that > have an orbital crossing exactly at the Fermi level. In such a case if the > exact position of the crossing is missed, the system appears to be an > insulator (or semiconductor). Any examples, references or even cartesian > coordinates for unit cells are greatly appreciated. > > > Example - 1D periodic (3,3) carbon nanotube > > * * > * * > * --- Fermi level > * * --- seeming top of the occupied bands if the crossing is missed > * * > A single sheet of graphite has pi and pi* bands touching at the Fermi level, at the edge of the BZ. That degeneracy arises from the crystal symmetry; isoelectronic BN has a band gap. Not sure what you mean by 'missing the exact position' though, for the degeneracy and therefore metallic behaviour will remain while the symmetry does even if electrons are added or removed. Graphite is strictly a semimetal as its DOS is zero at the Fermi level (near zero for the 3D crystal). David *************************************************************************** * Dr.David Parry E-MAIL * * d.e.parry@bristol.ac.uk * * School of Chemistry * * University of Bristol Office telephone Departmental numbers * * Cantock's Close +44 117 9546863 +44 117 9289000 voice * Bristol BS8 1TS +44 117 9250612 FAX * * UK * *************************************************************************** From chemistry-request@server.ccl.net Wed Dec 5 08:31:18 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5DV7i19176 for ; Wed, 5 Dec 2001 08:31:09 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id fB5DUn430654 for ; Wed, 5 Dec 2001 15:30:50 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Wed, 5 Dec 2001 15:30:49 +0200 (EET) From: Arvydas Tamulis To: Subject: help in formulae of Gaussian98 rho-ci Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Would you please to help me sending formulae and short description of rho-ci density in Gaussian98. I know that this is described in book "Exploring Chemistry with Electronic Structure Methods" chapter 9 but I have not this book. Maybe this rho-ci is also described in other books or articles? Please send me these rho-ci description pages by faxes: +370-2-225361 or +370-2-224694 or by e-mail tamulis@itpa.lt Thank you very much in advance for this indeed not pleasure work. With best regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +370-9919397 ******************************************************************* From chemistry-request@server.ccl.net Wed Dec 5 10:50:35 2001 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5FoYi21353 for ; Wed, 5 Dec 2001 10:50:34 -0500 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id QAA07615; Wed, 5 Dec 2001 16:47:15 +0100 (MET) for Received: from localhost (rvivasre@localhost) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id QAA05927; Wed, 5 Dec 2001 16:50:18 +0100 (MET) for Date: Wed, 5 Dec 2001 16:50:17 +0100 (MET) From: Ricardo Vivas-Reyes To: chemistry@ccl.net Subject: BSSE for ECP Calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL users, I am running a tin complex using Gaussian 98, that uses the LanL2DZ basis set for Sn and 6-31G* for all the other atoms in the complex. Now I am trying to run a BSSE calculation for this complex using the following input: #P B3LYP/Gen Massage Pseudo=Read -1 1 Molecular specification Sn LanL2DZ **** C H **** Sn LanL2Dz Which always ends with an error. Can you point me to a possible solution? Thank you in advance, Best wishes Ricardo. From chemistry-request@server.ccl.net Wed Dec 5 11:17:42 2001 Received: from electra.cc.umanitoba.ca (root@[130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5GHgi21800 for ; Wed, 5 Dec 2001 11:17:42 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with SMTP id KAA18304 for ; Wed, 5 Dec 2001 10:17:31 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Re: Prediction of Chemical Reactivity Date: Wed, 5 Dec 2001 10:17:31 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Whoa! Predicting reactivity is one hell of a problem especially if you want to cover such a wide range of systems. There are many programs that can help you to find reasonable structures for transition states, and more or less plausible activation energies. But to quantitatively predict relative rates simply from the identities of reactant pairs is not trivial! I don't think anyone can do it in a meaningful way. We are working on a "simple" problem related to case 1 below - nucleophilic substitution of primary alkyl chlorides. Believe me, it is consuming large amounts of high powered computer time, and we still haven't convinced referees that we are right in our explanation of the relative reactivities (although I am sure that we are ;-) )! You are not going to find this sort of thing "off the shelf". William Laidig Wrote: >I have a colleague who needs software forpredicting the probability of a aqueous >chemical reaction occurring between a variety of reactive chemicals at around >pH7. Specificly, > 1)nucleophilic substitiution of halogenated compounds > 2) Schiff base formaiton > 3) addition-elimination of acids, esters, amides > 4) nucleophilic adition of aldehydes and ketones > 5) Michael addition of alpha,beta unsaturated compounds > 6) addition by ring cleavage of epoxides > 7) electrophilic substitiution of diazonium salts >I am not up on current synthetic prediction program and would appreciate am >pointers to current software, recommendations, etc. I will summarize responsews >to the list Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@server.ccl.net Wed Dec 5 12:03:32 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5H3Wi22739 for ; Wed, 5 Dec 2001 12:03:32 -0500 Received: from silicon.chem.ucla.edu (silicon.chem.ucla.edu [169.232.135.10]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fB5H3LC28800 for ; Wed, 5 Dec 2001 09:03:21 -0800 (PST) Received: from localhost (mdb@localhost) by silicon.chem.ucla.edu (8.11.1/8.11.1) with ESMTP id fB5H3QT15778 for ; Wed, 5 Dec 2001 09:03:26 -0800 (PST) X-Authentication-Warning: silicon.chem.ucla.edu: mdb owned process doing -bs Date: Wed, 5 Dec 2001 09:03:26 -0800 (PST) From: "Michael D. Bartberger" To: Computational Chemistry List Subject: Re: CCL:Prediction of Chemical Reactivity In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You may wish to check the current status of the "CAMEO" program system, as developed by the Jorgensen group at Yale. Perhaps this might be helpful to you. Best regards, -Mike On Wed, 5 Dec 2001, Phil Hultin wrote: > Whoa! Predicting reactivity is one hell of a problem especially if you want > to cover such a wide range of systems. There are many programs that can > help you to find reasonable structures for transition states, and more or > less plausible activation energies. But to quantitatively predict relative > rates simply from the identities of reactant pairs is not trivial! I don't > think anyone can do it in a meaningful way. > > We are working on a "simple" problem related to case 1 below - nucleophilic > substitution of primary alkyl chlorides. Believe me, it is consuming large > amounts of high powered computer time, and we still haven't convinced > referees that we are right in our explanation of the relative reactivities > (although I am sure that we are ;-) )! You are not going to find this sort > of thing "off the shelf". > > > William Laidig Wrote: > > >I have a colleague who needs software forpredicting the probability of a > aqueous > >chemical reaction occurring between a variety of reactive chemicals at > around > >pH7. Specificly, > > 1)nucleophilic substitiution of halogenated compounds > > 2) Schiff base formaiton > > 3) addition-elimination of acids, esters, amides > > 4) nucleophilic adition of aldehydes and ketones > > 5) Michael addition of alpha,beta unsaturated compounds > > 6) addition by ring cleavage of epoxides > > 7) electrophilic substitiution of diazonium salts > >I am not up on current synthetic prediction program and would appreciate am > >pointers to current software, recommendations, etc. I will summarize > responsews > >to the list > > Dr. Philip G. Hultin > Associate Department Head and > Associate Professor of Chemistry > University of Manitoba > Winnipeg, MB, Canada R3T 2N2 > (vox) 204-474-9814 > (fax) 204-474-7608 > mailto:hultin@cc.umanitoba.ca > http://www.umanitoba.ca/chemistry/ > > > -= 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 Dec 5 08:21:50 2001 Received: from mail9.messagelabs.com ([194.205.110.133]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fB5DLni18994 for ; Wed, 5 Dec 2001 08:21:49 -0500 X-VirusChecked: Checked Received: (qmail 9298 invoked from network); 5 Dec 2001 13:20:48 -0000 Received: from mail04.europe.csc.com (194.133.99.131) by server-17.tower-9.messagelabs.com with SMTP; 5 Dec 2001 13:20:48 -0000 Received: by mail04.europe.csc.com (8.8.8+Sun/SMI-SVR4) id NAA13757; Wed, 5 Dec 2001 13:33:00 GMT Received: from av-int.eu.csc.com (192.168.140.24) by CSCgw. ID xai013677; Wed, 5 Dec 01 13:32:53 GMT Received: from ukhx48.avecia.com (unverified) by av-is-sweeper.aveciais (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Wed, 5 Dec 2001 13:21:08 +0000 Received: by UKHX48 with Internet Mail Service (5.5.2653.19) id ; Wed, 5 Dec 2001 13:20:04 -0000 Message-ID: <67DFB9481700D111900E00805F59F861038D98B5@UKHX14> From: Tackley Daniel R To: "Comp Chem Mailing List (E-mail)" Subject: TD-DFT Date: Wed, 5 Dec 2001 13:20:04 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="windows-1252" Dear All, Does anyone have any experience / hints that they could share on running TD-DFT calculations in Gaussian98? I am having problems with the Davidson convergence in that the TD step is constantly restarting with the following error message: Davidson failed to converge within maximum sub-space dimensions Restart with updated initial guess The updated guess shows no real changes from the previous gues and is certainly not the value obtained in the iteration just run. Are there any additional options that can be used (IOp's)? Does the functional and basis set used have a large effect. Thanks for your help, Daniel -- Dr Daniel Tackley Avecia Computational Chemistry Group Email: daniel.tackley@avecia.com Telephone: +44 161 721 2541 _____________________________________________________________________ This message has been checked for all known viruses on behalf of Avecia by the MessageLabs Virus Scanning Service. For further information visit http://www.messagelabs.com/stats.asp From chemistry-request@server.ccl.net Wed Dec 5 12:11:37 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5HBai22967 for ; Wed, 5 Dec 2001 12:11:36 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 34155154CE; Thu, 6 Dec 2001 01:11:24 +0800 (CST) Date: Thu, 6 Dec 2001 01:11:24 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: Gaussian 98 benchmark for PC systems Message-ID: <20011206011124.A19953@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hi, A brief preview of our benchmark results of Gaussian 98 for PC systems can be found at: http://oxygen.chem.nthu.edu.tw/~jsyu/benchmark/g98-index.html We have performed the benchmark for several machines including the combinations of AMD Athlon+SDRAM, Athlon+DDR, Athlon+dual-channel-DDR, and Intel Pentium4+RDRAM. The results of Alpha and SGI are listed also for comparison. More details will follow in weeks. Sincerely, -- Yu, Jen-Shiang Kenny // jsyu@Platinum.chem.nthu.edu.tw Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN From chemistry-request@server.ccl.net Wed Dec 5 16:45:50 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5Ljni27612 for ; Wed, 5 Dec 2001 16:45:50 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id QAA06343; Wed, 5 Dec 2001 16:45:39 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 05 Dec 2001 16:44:51 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GNW00F8R47CG2@lvlmail.unitedcatalysts.com>; Wed, 05 Dec 2001 16:40:24 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 05 Dec 2001 16:44:43 -0500 Content-return: allowed Date: Wed, 05 Dec 2001 16:44:43 -0500 From: "Shobe, Dave" Subject: RE: Predictionj of chemical reactivity To: "'laidig.wd@pg.com'" , "'chemistry@ccl.net'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15771@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Just by coincincidence I got this notice from CambridgeSoft today: ------------------------ 3. Cameo Comes to Windows ------------------------ One of the most useful applications of artificial intelligence to organic chemistry is to design syntheses of big and hairy molecules. Perhaps the next most useful is to identify and rectify the weak steps in a proposed scheme before any reagents are committed to flasks. To this end, the CAMEO program is used by a variety of chemical and pharmaceutical companies to shed light on their syntheses. Given starting materials and reaction conditions, CAMEO predicts the various reaction products, accompanied by comments explaining factors affecting their yield. Hitherto it has been available on VAX/VMS, Unix (Sun, SGI and AIX), and the Macintosh. CambridgeSoft is now porting the application to Windows using Excel as part of the front (i.e. display) end. Read more about this exciting product development at: http://chemnews.cambridgesoft.com/art.cfm?S=160 or email software@cambridgesoft.com for more information From chemistry-request@server.ccl.net Wed Dec 5 13:32:36 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5IWZi24581 for ; Wed, 5 Dec 2001 13:32:36 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA30531; Wed, 5 Dec 2001 13:32:21 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 05 Dec 2001 13:31:34 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GNV00DDHV97CU@lvlmail.unitedcatalysts.com>; Wed, 05 Dec 2001 13:27:07 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 05 Dec 2001 13:31:26 -0500 Content-return: allowed Date: Wed, 05 Dec 2001 13:31:26 -0500 From: "Shobe, Dave" Subject: RE: Predictionj of chemical reactivity To: "'laidig.wd@pg.com'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15770@lvlxch01.unitedcatalysts.com> 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 fB5IWai24582 I remember a program called Cameo (WL Jorgensen et al) that predicted the products of a reaction mixture. I think it used rho-and-sigma-type substituent effects for calculation of reaction rates and equilibria rather than any quantum calculations. There is still a home page for Cameo at http://zarbi.chem.yale.edu/products/cameo/ if you're interested. I don't know what's been written since then (and probably I only know about Cameo because I used to know some of the people that worked on the project). --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: laidig.wd@pg.com [mailto:laidig.wd@pg.com] Sent: Monday, December 03, 2001 3:39 PM To: chemistry@ccl.net Subject: CCL:Predictionj of chemical reactivity All, I have a colleague who needs software forpredicting the probability of a aqueous chemical reaction occurring between a variety of reactive chemicals at around pH7. Specificly, 1)nucleophilic substitiution of halogenated compounds 2) Schiff base formaiton 3) addition-elimination of acids, esters, amides 4) nucleophilic adition of aldehydes and ketones 5) Michael addition of alpha,beta unsaturated compounds 6) addition by ring cleavage of epoxides 7) electrophilic substitiution of diazonium salts I am not up on current synthetic prediction program and would appreciate am pointers to current software, recommendations, etc. I will summarize responsews to the list Thanks, Bill William D. Laidig CADMol Group Corporate Analytical CR-TD 513-627-2857 513-627-1233 (FAX) laidig.wd@pg.com -= 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 Dec 5 17:05:00 2001 Received: from hotmail.com ([64.4.9.209]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5M50i28129 for ; Wed, 5 Dec 2001 17:05:00 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 5 Dec 2001 14:04:44 -0800 Received: from 151.197.236.68 by lw9fd.law9.hotmail.msn.com with HTTP; Wed, 05 Dec 2001 22:04:44 GMT X-Originating-IP: [151.197.236.68] From: "James Ianni" To: chemistry@ccl.net Subject: KINTECUS V2.69 with Graphical Interface Date: Wed, 05 Dec 2001 17:04:44 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 05 Dec 2001 22:04:44.0754 (UTC) FILETIME=[D8D83320:01C17DD8] KINTECUS V2.69 ============================================================ A new version of Kintecus V2.69 is out! A GRAPHICAL INTERFACE has been devised for Kintecus. Examples can be viewed at http://www.kintecus.com/graphica.htm Now all one has to do to run a model is click a button! You can examine various screenshots of the new graphical interface under the "What's New" Page at www.kintecus.com. In addition, a new User Area has been created for User Created/Submitted Kintecus Material/Papers/Homework. As always, http://www.kintecus.com contains the latest versions of Kintecus, more models, pre-post processing, online documentation, custom Kintecus newsgroups and postings, current bug reports and forms, suggestion boxes, movies and much more! KINTECUS ============================================================ Powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other processes via a graphical interface. Kintecus features the ability to quickly run Chemkin/SENKIN II/III models without the use of supercomputing power or FORTRAN compiling/linking. Multiple Chemkin/freestyle thermodynamic databases can be used. Isothermal/Non-isothermal, adiabatic constant volume, constant pressure (variable volume) can easily be modeled with a flick of a switch. Programmed volume (replicating engine piston motion), programmed temperature, programmed species concentration can all easily be included in your model WITHOUT C/FORTRAN programming. Heterogeneous chemistry is also easily modeled. Now can now fit or optimize rate constants, initial concentrations, Lindemann/Troe/SRI/LT parameters, enhanced third body factors, initial temperature, residence time, energy of activation and many other parameters against your experimental/fabricated dataset(s). Kintecus V2.69 has the ability to fit/optimize rate constants, initial concentrations, Lindemann/Troe/SRI/LT parameters, enhanced third body factors, initial temperature, residence time, energy of activation and many other parameters against your dataset(s). Note that Kintecus will actually fit the parameters at EXACTLY the time your data was measured. Unlike other programs, Kintecus DOES NOT interpolate a function against your data and then fit the values against this interpolation. There is no need to ?clean? your data, suggest interpolation methods nor specify timing meshes against your experimental data since Kintecus calculates values at exactly the times you specify in your experimental datafile. Kintecus is a compiler to model the reactions of chemical, biological, enzyme, nuclear and atmospheric processes using three input spreadsheet files: a reaction spreadsheet, a species description spreadsheet and a parameter description spreadsheet. For thermodynamics, an optional thermodynamics description spreadsheet can be supplied. Kintecus has been designed with ease of use in mind. Absolutely no programming, compiling or linking required. KEYWORDS: Combustion Software, chemical kinetics software, enzyme kinetics, pharmakinetics software, GRI-MECH software, thermodynamics, sensitivity analysis, simulation software _____________________________________________________ jci10@hotmail.com Dr. James Ianni, MS., Ph.D. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Dec 5 18:34:22 2001 Received: from electra.cc.umanitoba.ca (root@[130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB5NYLi29554 for ; Wed, 5 Dec 2001 18:34:22 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with SMTP id RAA15513 for ; Wed, 5 Dec 2001 17:34:10 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Reactivity and Expert Systems Date: Wed, 5 Dec 2001 17:34:08 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Michael Bartberger and others have suggested CAMEO as a viable way of predicting reactivity. I have not seen CAMEO recently, and I certainly do not intend to "diss" it or its creators. As I understand it, CAMEO is a sort of "expert system" based on empirical rules. This may well be the sort of prediction that William Laidig was seeking, and there is nothing wrong with that. Perhaps I understood the question about "predicting reactivity" in a different context than was meant. An "expert system" is only as good as its rules when it comes to addressing chemical systems outside the range of structures that went into its parameterization. Unfortunately, many of the "rules and rationalizations" that we learned as undergraduates and that are still widely used by research chemists are simply incorrect at a fundamental level, particularly as they apply to reactions in solution. While they are in many cases qualitatively successful, the fundamental flaws in their logic mean that they will fail for some (unknown) set of situations. If you don't agree with this assertion about "rules and rationalizations", you should consider the usual explanation organic chemists use for the differing acidities of organic acids. If it was true that acidities could be correctly understood in terms of delocalization of charge in the conjugate base (by inductive withdrawal or by resonance), then a) gas-phase acidities and solution phase acidities would show parallel trends (they do not in general) and b)the trend would be reflected in the enthalpies of ionization in solution (it is not, in general). The data on this have been available for decades and can be found in standard (older) physical organic textbooks as well as compendia of physical data. So, to return to my argument about reactivity, if we base our analysis of an unknown reaction on rationalizations that are based on questionable (or false) premises, are we actually able to predict its behavior? Or are we simply lucky? Speaking as an experimental organic chemist who has turned recently to computational chemistry to find answers to nagging questions that conventional wisdom (at least among organic chemists!) has not adequately addressed, I still maintain that accurate prediction of reactivity remains a highly challenging problem that is not really dealt with by off-the-shelf solutions. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/