From chemistry-request@server.ccl.net Thu Aug 16 21:29:42 2001 Received: from smtp-4.ig.com.br ([200.226.132.153]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7H1Tev11598 for ; Thu, 16 Aug 2001 21:29:41 -0400 Message-Id: <200108170129.f7H1Tev11598@server.ccl.net> Received: (qmail 29263 invoked from network); 17 Aug 2001 01:16:26 -0000 Received: from webmail-9.ig.com.br (HELO localhost) (200.225.157.214) by smtp-4.ig.com.br with SMTP; 17 Aug 2001 01:16:26 -0000 Date: Thu, 16 Aug 2001 22:16:30 -0300 To: chemistry@ccl.net From: perott@ig.com.br Cc: X-Originating-IP: [200.225.157.214]200.213.78.184 X-Mailer: InMail by Insite - www.insite.com.br X-user: perott@ig.com.br Subject: Post-HF in ab initio calculations of solids Dear CCLers, I wonder is there any program available for the post-HF treatment of electronic correlation in ab initio calculations of solids? I'll summarize! Thanks! Claudio. ---------------------------------------------- Claudio A. Perottoni Universidade Federal do Rio Grande do Sul Instituto de Fisica Av. Bento Goncalves, 9500 91501-970 Porto Alegre - RS BRAZIL http://www.if.ufrgs.br/~perott/index.html ---------------------------------------------- _________________________________________________________ Oi! Você quer um iG-mail gratuito? Então clique aqui: http://registro.ig.com.br/ From chemistry-request@server.ccl.net Thu Aug 16 14:43:59 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7GIhtv05345 for ; Thu, 16 Aug 2001 14:43:56 -0400 Received: from ppp-212.56.193.59.mldnet.com (ppp-212.56.193.59.mldnet.com [212.56.193.59]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id VAA27605 for ; Thu, 16 Aug 2001 21:43:49 +0300 Date: Sun, 16 Sep 2001 21:47:39 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <1202203846.20010916214739@yahoo.com> To: chemistry@ccl.net Subject: calculated spectra MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, I have one (may be dummy question) on calculated UV/Vis spectra. I use ArgsuLab 2.0.0. for calculation of spectra. As a result I get smth like that (see below). Here are my questions: * How could I compare Oscillator Strength data with lg e values from experiment? * Where could I find description of length, velocity and Hansen Oscilator Strength? * Could anybody point me references on TDA and RPA excited state analysis? Thanks. 2 ( 1)->( 2) Energy 18616.3 cm-1, (537.2 nm) State Dipole 5.2354 Oscillator Strength length 0.0003 velocity 0.0055 Hansen 0.0012 Rot. Str. 0.0540 State Dipole 2.8518 1.3304 -4.1840 Transition Dipole Electric (length) 0.0885 -0.1416 0.0399 Electric (velocity) 0.0281 -0.0605 0.0056 Magnetic (au, velocity) 0.5808 0.1978 0.0426 Wiberg Atom-Atom Bond Orders ***************************** [skip] Mulliken Atomic Charges ************************ [skip] Occ. MO -> Unocc. MO ********************** ( 19) -> ( 28) 0.061150 ( 24) -> ( 28) -0.152007 ( 24) -> ( 29) -0.069248 ( 24) -> ( 30) -0.065480 ( 24) -> ( 31) 0.224257 ( 24) -> ( 34) 0.051147 ( 25) -> ( 28) -0.910024 ( 25) -> ( 30) 0.220747 ( 25) -> ( 31) 0.105606 ( 25) -> ( 34) 0.061978 ( 26) -> ( 28) 0.116210 Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Thu Aug 16 21:07:02 2001 Received: from mail.etang.com ([202.101.42.207]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7H171v11338 for ; Thu, 16 Aug 2001 21:07:01 -0400 Received: from ns (unknown [202.108.240.3]) by mail.etang.com (Postfix) with ESMTP id 5C6641C548C02; Fri, 17 Aug 2001 09:15:12 +0800 (CST) Message-ID: <002a01c126b8$b46f1020$cd0b140a@fudan.edu.cn> From: "jewar" To: "tianxiao young" , References: Subject: Re: CCL:ab initio MD code Date: Fri, 17 Aug 2001 09:05:27 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f7H172v11339 Dear Yang, There are some website about the ab initio MD programs. FHI: http://www.fhi-berlin.mpg.de/th/th.html VASP: http://cms.mpi.univie.ac.at/vasp/ CASTEP: http://www.tcm.phy.cam.ac.uk/castep/ Good Luck! Yun Wang Dept.of Chem. Fudan University From chemistry-request@server.ccl.net Fri Aug 17 03:21:27 2001 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7H7LRv15537 for ; Fri, 17 Aug 2001 03:21:27 -0400 Received: from unibas.ch (filou.chemie.unibas.ch [131.152.112.19]) by igor.urz.unibas.ch (PMDF V6.0-24 #41480) with ESMTP id <0GI700H4PB3QEO@igor.urz.unibas.ch> for chemistry@ccl.net; Fri, 17 Aug 2001 09:21:26 +0200 (MET DST) Date: Fri, 17 Aug 2001 09:20:25 +0200 From: Stanislav Ivan Subject: ForceField:summary To: chemistry@ccl.net Message-id: <3B7CC5B9.D55B2CC2@unibas.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.75 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCL'ers, thank you very much for your advices.Following is my former question and all of replies. Dear CCLers, I am PhD student and I am just starting calculations using Force Field methods. Could you please advice/suggest me some basic references about Force Field with the description of basic methods (AMBER, MM2 etc.) and their preformance on different systems (proteins,DNA, general organic systems), reliability of such calculations, .... Thanks in advance. Stanislav Ivan Institut fur Organische Chemie 4056 Basel Switzerland stanislav.ivan@unibas.ch *********************************************************************************** Get the book by Andre Leach "Molecular Modelling" (Longman publishers) -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *********************************************************************************** I would recommend the following; 1. "Computational Chemistry; A practical guide to applying techniques to real world problems. ", David Young, Wiley-Interscience, 2001 This is a new but very good book. A bit quantum focussed, but still good. 2. "Molecular Modeling: Principles and Applications", AR Leach, 1996, Essex, Addison Wesley Longman Limited A much more robust book (595 pp) that goes into more detail than Grant and Richards. Gives more examples and a more solid theoretical foundation for the techniques. My choice for a graduate level textbook. 3. "Dynamics of Proteins and Nucleic Acids," JA McCammon and SC Harvey, 1987, Cambridge, Cambridge University Press. Always a classic - an excellent (though a little dated) description of simulations of proteins and nucleic acids. Good low level introductions to theory with some nice examples and applications. Dr. Shyam Vyas Applications Scientist Accelrys Inc. (formerly Molecular Simulations Inc) 300 Lanidex Plaza, 3rd Floor Parsippany, New Jersey 07054 Phone: 973-386-5549 Fax: 973-386-5584 Email: svyas@accelrys.com Mobile: 1-201-738-4137 *********************************************************************************** Regarding your request for information on force fields, you might want to check out Reviews in Computational Chemistry. This book series has had a number of chapters on force fields, molecular mechanics, and simulations. Two of these chapters are: I. Pettersson and T. Liljefors, in Reviews in Computational Chemistry, VCH, New York, 1996, Vol. 9, pp. 167-189. Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields. M. Jalaie and K. B. Lipkowitz, in Reviews in Computational Chemistry, Wiley-VCH, New York, 2000, Vol. 14, pp. 441-486. Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations. Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Gordon Research Conferences on Computational Chemistry http://chem.iupui.edu/rcc/grccc.html Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu *********************************************************************************** Two nice tutorials on the topic of force fields exist in Reviews in Computational Chemistry, Volume 2, 1991, VCH Publishers (now Wiley-VCH). Chapter 4: New Approaches to Empirical Force Fields by Dinur and Hagler and Chapter 3: Molecular Mechanics: The Art and Science of Parameterization by Bowen and Allinger. An assessment of how well different force fields do for different types of problems has been reviewd in that book series (Volume 9, published in 1996) by Peetterson and Liljefors. A fairly up to date listing of publications in which force field parameters have been published exists as an appendix in Volume 14 (published by Wiley VCH in 2000). There exist several stellar books on the topic of force fields as well but these aforementioned chapters are designed as tutorial-type reviews which are quick to read. Lipkowitz lipkowitz@chem.iupui.edu *********************************************************************************** CHARMM22 All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616 OPLS Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides J. Phys. Chem. B 2001, 105, 6474-6487 Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids J. Phys. Chem. 1996, 100, 18010-18013 Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 Lic. Marcos Villarreal Grupo de Biofisica Departamento de Quimica Biologica Facultad de Ciencias Quimicas Universidad Nacional de Cordoba Ciudad Universitaria (5000) Cordoba Argentina *********************************************************************************** Gundertofte et al., Journal of Computational Chemistry Vol 17 No 4, 429-49 (1996) M.D. Beachy et al., Journal of the American Chemical Society, Vol. 119, 5908-5920 (1997) -- Eric Bennett ( ericb@pobox.com ; http://www.pobox.com/~ericb ) *********************************************************************************** You might read "Molecular Mechanics Across chemistry", by Rappe and Casewit, 1997. E. Lewars *********************************************************************************** Study the book of Jensen (Introduction to Computational Chemistry), or Leach (Molecular Modelling: Principles and Applications). -- Marcel Swart Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB) Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen The Netherlands *********************************************************************************** From chemistry-request@server.ccl.net Fri Aug 17 07:45:49 2001 Received: from wyoming.com ([199.190.151.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HBjnv02208 for ; Fri, 17 Aug 2001 07:45:49 -0400 Received: from [204.227.221.60] (account madscientist HELO wyoming.com) by wyoming.com (CommuniGate Pro SMTP 3.4.7) with ESMTP-TLS id 37432965 for CHEMISTRY@ccl.net; Fri, 17 Aug 2001 05:45:47 -0600 Message-ID: <3B7D03DC.1CAE1719@wyoming.com> Date: Fri, 17 Aug 2001 05:45:33 -0600 From: Philip Stortz Reply-To: madscientist@wyoming.com Organization: Thub R/D X-Mailer: Mozilla 4.75C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: crystal/electronic spectra References: <002a01c126b8$b46f1020$cd0b140a@fudan.edu.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit does any one know if the crystal program or mos-f are really good at predicting electronic spectra? i'd like to find a program that can do a good job on a wide variety of bulk solids without having to tweak the constants all the time. of course any other program that works well would be fine. i know this is a hard problem to solve and last time i looked another was that useful, i'd like to save lab time, not use it to modify constants. thanks. -- "To invent, you need a good imagination and a pile of junk." --Thomas Edison Philip Stortz, Mad_Scientist_at_Large. available to take over worlds large or small. From chemistry-request@server.ccl.net Fri Aug 17 09:54:58 2001 Received: from smtp2.libero.it ([193.70.192.52]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HDswv04733 for ; Fri, 17 Aug 2001 09:54:58 -0400 Received: from libero.it (151.21.176.157) by smtp2.libero.it (5.5.031) id 3B3A187200972FF0 for chemistry@ccl.net; Fri, 17 Aug 2001 15:54:52 +0200 Message-ID: <3B7D240A.A1EF7577@libero.it> Date: Fri, 17 Aug 2001 16:02:51 +0200 From: Tiziano Tarpanelli X-Mailer: Mozilla 4.51 [it] (Win98; I) X-Accept-Language: it MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:2-indanone/crystal structure? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, in the last weeks I spend a lot of time for searching literature about the crystal structure of 2-indanone [CAS: 615-13-4], but I did not find an answer. So: Does anybody know something about the CRYSTAL STRUCTURE of this small and nice molecule (parameters, space group, exp. and theoretical data,...) ? Thank you very much. Best regards Tiziano From chemistry-request@server.ccl.net Fri Aug 17 11:42:09 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HFg7v07160 for ; Fri, 17 Aug 2001 11:42:08 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15Xll5-0004CE-00; Fri, 17 Aug 2001 17:42:03 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id SAA25826 for ; Fri, 17 Aug 2001 18:02:17 +0200 (GMT) Date: Sat, 18 Aug 2001 05:41:38 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <13210053547.20010818054138@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: multiplisity in 5-coordinate Fe of Heme ??? In-reply-To: <3B73B412.000001.26412@smtp1> References: <3B73B412.000001.26412@smtp1> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCL'ers, Could anyone briefly explain why heme - the active site of peroxidases - in resting state has open shell on iron (unpaired electron) ??? And what the total charge is of the total fragment (the propionic residues of porphirin isn't dissociated) and why? The articles I share there is no detailed explanation about the nature of resting site and, along, I am not smart enough in transition metal chemistry ... P.S. The active site is composed of heme (Fe III), axial (proximal) ligand (His). One could point to the reference about the study on the electronic structure of the heme in peroxidases too. From chemistry-request@server.ccl.net Fri Aug 17 06:04:13 2001 Received: from sina.com ([202.108.35.242]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7HA4Cv21950 for ; Fri, 17 Aug 2001 06:04:12 -0400 Received: (qmail 12385 invoked by uid 99); 17 Aug 2001 10:01:27 -0000 Message-ID: <20010817100127.12384.qmail@sina.com> From: cgliu To: chemistry@ccl.net Subject: Conformation search software wanted. Date: Fri, 17 Aug 2001 18:01:27 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 2 Dear cclers: I am preparing to work on the conformation analysis for the peptides, especially, those cyclic ones. Does anyone know any softwares, which are stable, fast,cheap or even free, and if possible, running parallelly on UNIX systems. Best regards Chungen ______________________________________ Chungen Liu, Dr. Chemistry Department Nanjing University Nanjing, 210093 China cgliu@sina.com =================================================================== ÐÂÀËÃâ·Ñµç×ÓÓÊÏä (http://mail.sina.com.cn) ¶©ÔÄÊÖ»ú¶ÌÐÅÍ·ÌõÐÂÎÅ£¬ÌìÌì½±¶à¿îʱÉÐÊÖ»ú£¡ (http://dailynews.sina.com.cn/c/272235.html) ÏëÈÃ100ÍòÄ°ÉúÈËͬʱ°®ÉÏÄãô?À´ÕÒÎÒ°É! (http://cheese.sina.com.cn) From chemistry-request@server.ccl.net Fri Aug 17 13:19:08 2001 Received: from email04.aon.at ([195.3.96.115]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7HHJ8v08726 for ; Fri, 17 Aug 2001 13:19:08 -0400 Received: (qmail 276696 invoked from network); 17 Aug 2001 17:19:02 -0000 Received: from n778p019.adsl.highway.telekom.at (HELO pc1.eidolon.net) ([62.47.41.51]) (envelope-sender ) by qmail4.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 17 Aug 2001 17:19:02 -0000 Sender: hal@pc1.eidolon.net To: chemistry@ccl.net Subject: Is my system equilibrated? From: Hannes Loeffler Date: 17 Aug 2001 19:19:05 +0200 Message-ID: <87wv421u5y.fsf@pc1.eidolon.net> Lines: 9 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Artificial Intelligence) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello CCLers, I'm looking for in-depth studies dealing with the problems of proper equilibration of MD systems, i.e. how long it takes until a system is equilibrated (if at all). Any hints? TIA, Hannes. From chemistry-request@server.ccl.net Fri Aug 17 07:10:01 2001 Received: from earth.ox.ac.uk (root@[163.1.22.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HBA0v01654 for ; Fri, 17 Aug 2001 07:10:00 -0400 Received: from pauling.earth.ox.ac.uk (pauling [163.1.22.22]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id MAA23351 for ; Fri, 17 Aug 2001 12:09:58 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15228.64389.348325.335076@gargle.gargle.HOWL> Date: Fri, 17 Aug 2001 12:09:57 +0100 To: Computational Chemistry List Subject: SUMMARY: Potential parameter fitting X-Mailer: VM 6.95-rfhacked under 21.1 (patch 12) "Channel Islands" XEmacs Lucid I received a few attempts to summarise the responses, so here is a brief summary. I asked what programs were avialable for potential parameter fitting to energy hypersurfaces, such as ab-initio energies. The main responses were 1. NBP by the late Prof D. E. Williams, http://www.louisville.edu/~dewill01/nbp.html This seems to be about the best suited program for such tasks. It used to be obtainable directly from Prof Williams, but none of my respondents had any idea how to obtain it now, as he recently passed away. I hope this does not become lost to the community. 2. A number of respondents pointed me to GULP by Julian Gale http://www.ch.ic.ac.uk/gale/Research/gulp.html which is slightly embarrassing since I thought I knew that program fairly well :) It can indeed be used to fit to an energy hypersurface (which I erroneously thought it wasn't well suited for). GULP uses a 3D periodic model, which isn't what I need for this particular calculation, (A simple isolated moecular cluster), but of course it's not to hard to achieve this by judicious use of a large supercell and interaction cutoffs and turning off the long-ranged part of coulomb interactions. 3. Though not what I was looking for Andrew Horsfield (horsfield@fecit.co.uk)suggested that The OXON tight binding package also fits (and implements) Tersoff type potentials. 4. "Kjeld Rasmussen studied with Lifson and has modified that august program over the years to be a parameter-fitting tool. It can fit to structural parameters and vibrational frequencies but i do not believe to a hypersurface. Kjeld readily gives the program away. Some of the background to his program is given at: [1]http://struktur.kemi.dtu.dk/cff/cffhome.html" 5. "Arnold Hagler had a similar program (I believe called "Probe") that also came from Lifson's program and it was modified to fit hypersurface data but I think it is now a proprietary commercial product for MSI consortium members." 6. Marcelo Zaldini has been "developing a methodology, called SJBR, to do the parametrization of the intermolecular terms (coulomb + lennard_jones), based upon ab initio calculations, in an automatic fashion." which he hopes to release at some future time, when it is finished. 7. Other co-respondents recommended general least squares fitting methods such as the least-squares module in Scientific Python, available from http://dirac.cnrs-orleans.fr/programs/scientific.html, or even gnuplot! Although of course the built-in fit is only 1-dimensional and therefore not suitable, the gnuplot FAQ contains links to a number of other general purpose leasy-squares programs, such as Fudgit. None of these really fulfil the spirit of my request which was for a program which handles the bookkeeping and set-up for molecular models. Thanks to Konrad Hinsen , Manuel Melle-Franco , Irena Efremenko , Andrew Rohl , Brian J. Teppen" , Marcelo Zaldini Hernandes , Daquan Gao Andrew Horsfield for the suggestions. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Fri Aug 17 09:08:59 2001 Received: from maverick.arl.army.mil ([128.63.58.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HD8wv03672 for ; Fri, 17 Aug 2001 09:08:59 -0400 Subject: G.S. Calculation for Radicals To: CHEMISTRY@ccl.net From: "Mark Zottola - Contractor" Date: Fri, 17 Aug 2001 09:07:57 -0400 Message-ID: X-MIMETrack: Serialize by Router on Maverick/arl(Release 5.0.8 |June 18, 2001) at 08/17/2001 09:07:58 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii I would like to calculate the structure of the methoxy radical. How can I determine whether the structure I calculate is in the ground state or an excited state? As I am interested in the energetics of a reaction involving this species, an accurate determination of GS vs ES is important. BTW, I am using coupled-cluster theory to calculate the structures I am interested in. Thanks for any help you can send my way. Mark ************************************************ Dr. Mark A. Zottola PET Director of Computational Chemistry and Materials Army Research Laboratory MSRC PB 191 939-I Beards Hill Road Aberdeen MD 21001 VOICE: 410 278 7250 FAX: 410 297 9521 From chemistry-request@server.ccl.net Fri Aug 17 15:57:04 2001 Received: from hotmail.com ([64.4.9.124]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7HJv4v11517 for ; Fri, 17 Aug 2001 15:57:04 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 17 Aug 2001 12:56:59 -0700 Received: from 151.197.234.247 by lw9fd.law9.hotmail.msn.com with HTTP; Fri, 17 Aug 2001 19:56:59 GMT X-Originating-IP: [151.197.234.247] From: "James Ianni" To: chemistry@ccl.net Subject: New Version of Kintecus V2.3 has been released... Date: Fri, 17 Aug 2001 15:56:59 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Aug 2001 19:56:59.0867 (UTC) FILETIME=[C6C6C2B0:01C12756] What's New in Kintecus V2.3 ? ============================== If you are a new user you may want to read the QUICK INTRO and "What can it do ?" section for a very quick introduction to Kintecus. For those, already familiar with Kintecus you can just read this section. The main new feature in Kintecus V2.3 is 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. Some other changes and additions have been added such as the ability to view the delta-S,H,G,Kp, kr of the reactions, and the H, S, G, Cp, Gas Density and other physical properties of system as the simulation runs. See the .pdf file for full descriptions. In addition, some users were complaining that the Freeform spreadsheet output of Chemkin thermodynamic databases didn't included Mw, so this has also been changed. A new MAP keyword, CMW, has been added to convert the empirical Mw data field into Kintecus Mw. For examples, see the ethanol combustion, O2-OH combustion, Ozone decomposition and GRI-MECH samples which all include this keyword. Again, please refer to the .pdf documentation for a full description of these new features in V2.3 and many other additions! QUICK INTRO ============ Powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other processes. There are many features. One prime feature is 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 V2.3 - What can it do ? ================================== Kintecus is a compiler to model the reactions of chemical, biological, 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. A quick overview of the main features: The ability to convert Chemkin-II/Chemkin-III/Senkin models to Kintecus format. Kintecus can run almost any converted Chemkin model. Once converted, you may apply any Kintecus feature to the system. Do not be surprised to see the converted system run much faster! In addition, Kintecus can use multiple Chemkin thermodynamic databases at the same time and provides a way to use “reserve” species to a respective thermodynamic database. One can also convert the databases to a “freeform” format, which can be loaded into Excel or Lotus 1-2-3. The “freeform” database is much easier to maintain and update. In addition, the converted model is not limited to several elements, in fact, your model can contain the entire Periodic Table. >>The ability to model thousands and thousands of reactions in a relatively short time. Kintecus has been used with models as large as 120,000+ chemical reactions. You will not find anything faster than Kintecus. >>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 absolutely 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. >>Full output of normalized sensitivity coefficients selectable at any specified time or times. Normalized sensitivity coefficients are used in accurate mechanism reduction, determining which reactions are the main sources and sinks (network analysis) and which also shows which reactions require accurate rate constants and which ones can have essentially guessed rate constants. >>The ability to use profiles or perturbations of any wave pattern for any species, temperature, volume or hv. Using profiles/perturbations can also be used for studying very realistic systems, such as quenching affects, dissolution of various gases into a system over time, induction of current into a system, heat flow into a system, a piston compressing the reaction chamber and so on. >>A powerful parser with mass & charge balance checker for those reactions that the graduate student "supposedly" entered in correctly but the model is yielding incorrect results or is divergent. Do you know a kinetics program that can completely parse and check for mass/charge balance on a reaction like this: Rate Constants , (m and Ea), REACTIONS: 1.234e-20, 1.2, 3000,CH3(((NO2)3(CO)93)3 (CH2)9)+23.30H2O+ + Co2 = A--- + B++++ +C+C+C+C+C Or how about this: Rate Constants , REACTIONS: 5.043e+20 , 3.43234 (CH4(N(PO342)43(CH3)3)34)(Os(S7)8)34++++ + 199.432 X++++ 5CH5+ ==>5.434 Some_Really_Funky_Long_Enzyme_Name+ 8 HCl + HCO3- Kintecus is able to accurately check the above reaction for mass and charge balance because you can create an optional name file containing common names for species and then their mass representation. This smart mass balance can be used for biological and nuclear reactions! Kintecus also provides duplicate reaction and species checking. >>As you can see in the above reaction, fractional coefficients for species! Now you can finally model that last step in the Oregonator or crunch 100 elementary reaction steps in one reaction step! >>Built in support for special reactions such as: reactions involving third-bodies (M), fall-off reactions (Troe, Lindemann, SRI, etc.) , enhanced third bodies, exclusive multiple enhanced third bodies, vibrational transfer reactions (Landau-Teller) and many others. >>Heterogeneous chemistry can be modeled. For example, a species in the aqueous phase will not contribute to the overall pressure in the system or be involved in third-body reactions or fall- off reactions. Gaseous species can “enter” other phases through out a simulation and vice-versa. >>Automatic generation of the species spreadsheet file using the reaction spreadsheet file. Why waste time finding, entering and initializing all the different species in your kinetic scheme? >>The ability to do reactions in a continuous stirred tank reactor (CSTR) with multiple inlets and outlets. >>The ability to compute all internal Jacobians analytically. This is very useful for simulating very large kinetic mechanisms (more than 50,000). Finite difference methods can cause underflow or overflow errors in approximately such large Jacobians during the simulation. >>Support for Excel and Lotus spreadsheet programs. WHERE TO GET ??? ===================================================== http://www.ccl.net/cca/software/MS-WIN95-NT/kintecus OR vtd.cc (click on Kintecus_2X link, you can also read the online .pdf documentation) OR kintecus.com (coming soon....) _____________________________________________________ Dr. James Ianni, MS., Ph.D. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp