From perera@qtp.ufl.edu Tue Nov 26 17:45 EST 1996 Received: from qtp.ufl.edu for perera@qtp.ufl.edu by bedrock.ccl.net (8.8.3/950822.1) id RAA22136; Tue, 26 Nov 1996 17:45:28 -0500 (EST) Received: from visi4.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id RAA09843; Tue, 26 Nov 1996 17:45:25 -0500 Received: by visi4.qtp.ufl.edu (SMI-8.6/4.11) id RAA14576; Tue, 26 Nov 1996 17:45:18 -0500 From: "Ajith Perera" Date: Tue, 26 Nov 1996 17:45:18 -0500 Message-Id: <199611262245.RAA14576@visi4.qtp.ufl.edu> To: chemistry@www.ccl.net Subject: Aces II workshop ********************************************************************** Dear Colleague: We are pleased to announce an ACES II Workshop, conducted by authors of the program, that will be held from January 12-15, 1997, at the University of Florida in Gainesville, Florida. Through a cooperative agreement with IBM., the workshop will be conducted on IBM 39H or equivalent. Further details are on the attached announcement or our web site (http://www.qtp.ufl.edu/ Aces2/wkshp) To take advantage of inexpensive plane fares that include a Saturday night stay, we have scheduled the workshop for Sunday through Wednesday, January 12-15, with your potential arrival on Saturday, January 11, 1997 and start of workshop will be Sunday afternoon. Recommended departure is on Thursday, January 16, 1997. The workshop is a "hands on course" which provides an opportunity to run a wide variety of calculations for various properties. The "hands on" lab experience will be coupled with a few overview lectures. We also devote time to hear about your research problems and try to assist you in using ACES II to help solve them. Social events include a welcoming cocktail/buffet Sunday evening and dinner Wednesday evening. Tuition, a group dinner, refreshments and detailed lecture notes, is at an inclusive $500.00 per person. Enrollment will be limited to 24 participants, housed at the Reitz Union on the University of Florida campus. Please make your own reservations at the Reitz Union Hotel (352-392-2151), but we will gladly assist. We have reserved a block of rooms for participants ranging from $38.00 to $50.00 per night. (Please refer to the ACES II Workshop when you make your reservations.) Although the course is intense, companions are invited to accompany a participant by payment of an additional $50.00 to cover the social affairs. If you are interested in registering for our workshop, please contact Kathy Fuller in my office at (352) 392-1598 or by e-mail (fuller@qtp.ufl.edu) as soon as possible. Reservations are on a first-come basis. The registration form plus a check or purchase order payable to the University of Florida Research Foundation will be required by December 30, 1996, and should be sent directly to me at the Quantum Theory Project, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435 We hope that you or some of your colleagues will find our course to be of interest. If we can provide any further information, please contact us Sincerely Rodney J. Bartlett Graduate Research Professor of Chemistry and Physics * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ACES II WORKSHOP January 12-15, 1997 - University of Florida - Gainesville, Florida Advanced Concepts in Electronic Structure II (ACES II) is a very fast, easily used program directed at high-level, correlated, ab initio studies of molecules. It offers the most modern methods based upon coupled-cluster (CC) theory and its finite-order, many-body perturbation theory (MBPT=MP) approximations; all augmented by analytical gradients; as well as density functional theory (DFT). The program offers many unique, recently developed methods that open new vistas for application (See course text for a summary of many ACES II applications, R. J. Bartlett and J.F. Stanton, "Application of Post-Hartree-Fock Methods: Atutorial ," in Reviews of Computational Chemistry, 5, P. 65, eds. D. Boyd and K. Lipkowitz, VCH publishers, New York, NY, (1994). All correlated calculations exploit symmetry through D2h, making the program unusually fast for applications to symmetric molecules. With the cooperation of IBM, this "hands-on" workshop will demonstrate how to perform correlated ACES II applications for the following topics: Energies, Molecular Structures, and Vibrational Spectra Electronic Excited States and UV-vis Spectra NMR Shielding Constants NMR Spin-Spin Coupling Constants Photoelectron Spectra Molecular Properties, like Moments, Spin Densities, Field Gradients, etc. Polarizabilities and Hyperpolarizabilities Transition State Searches and Activation Barriers Visualization of Molecular Densities and Related Quantities And many other topics... All the above apply the newest techniques based on coupled-cluster (CC) theory, including triple excitations, with restricted, restricted open shell, unrestricted, and quasi-restricted (RHF, ROHF, UHF, QRHF) reference functions with analytical gradients; for excited states, the new equation-of-motion coupled-cluster (EOM-CC) theory and the two-determinant (TD-CC) theory; for ionization and electron attachment processes (EOM-IP CC and EOM-EA CC); for first-order properties, the CC/MBPT "relaxed density" approach; and for second-order properties, EOM-CC. The methods are described in overview lectures followed by supervised applications on IBM 39H or equivalent designed to illustrate the approach. Time is also provided to enable you to investigate your own applications with expert assistance. We also address topics like computer resource management. Attendance is limited to 24 people on a first-come basis. For further information: Rodney J. Bartlett Quantum Theory Project University of Florida P. O. Box 118435 Gainesville, FL 32611-8435 (904) 392-1597 or aces2@qtp.ufl.edu or our web site http://www.qtp.ufl.edu/Aces2/wkshp From ajit@unb.ca Sat Nov 23 06:48:44 1996 Received: from unb.ca for ajit@unb.ca by www.ccl.net (8.8.3/950822.1) id FAA29616; Sat, 23 Nov 1996 05:51:22 -0500 (EST) Received: (from ajit@sol.sun.csd.unb.ca [131.202.3.6]) by unb.ca (8.7.6/961016-08:40) id GAA11788 for ; Sat, 23 Nov 1996 06:51:23 -0400 (AST) Received: from localhost by jupiter.sun.csd.unb.ca (8.8.3/960921-23:43) id GAA03349; Sat, 23 Nov 1996 06:51:22 -0400 (AST) Date: Sat, 23 Nov 1996 06:51:21 -0400 (AST) From: "Ajit J. Thakkar" X-Sender: ajit@sol.sun.csd.unb.ca To: chemistry@www.ccl.net Subject: Free student HMO calculator Message-ID: I have uploaded to Simtel.Net: http://www.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip ftp://ftp.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip 103636 bytes hmo10.zip Student Huckel molecular orbital calculator HMO performs Huckel theory calculations on planar conjugated hydrocarbons. Undergraduate students find HMO easy to learn and use. HMO accepts input interactively with helpful suggestions. It traps and diagnoses common student input errors. HMO calculates molecular orbital coefficients and energies, pi-electron populations (densities), bond orders, bond lengths, free valences and self polarizabilities. Basic information on use of reactivity indices is presented. HMO requires less than 120KB of free memory. Freeware. Ajit J. Thakkar, Chemistry Department, University of New Brunswick ajit@unb.ca http://www.unb.ca From armel@fluo.univ-lemans.fr Mon Nov 25 08:49:11 1996 Received: from ciripa.idris.fr for armel@fluo.univ-lemans.fr by www.ccl.net (8.8.3/950822.1) id HAA13479; Mon, 25 Nov 1996 07:59:35 -0500 (EST) Received: from fluo.univ-lemans.fr (fluo.univ-lemans.fr [193.52.30.128]) by ciripa.idris.fr (8.8.3/8.8.3) with SMTP id NAA29602 for ; Mon, 25 Nov 1996 13:59:17 +0100 Received: from pcb4122.univ-lemans.fr by fluo.univ-lemans.fr (AIX 3.2/UCB 5.64/4.03) id AA15407; Mon, 25 Nov 1996 13:57:07 +0100 Message-Id: <1.5.4.32.19961125125953.006716e4@fluo.univ-lemans.fr> X-Sender: armel@fluo.univ-lemans.fr (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Nov 1996 13:59:53 +0100 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Re: CCL:fortran/PC Dear CCL fellows, Fredrik B|kman write: >Hints on what FORTRAN >compilers that are good (or even: available) >for pentium/windows95 systems would be greatly >appreciated. I use a C compiler (MSVC++2.00) on Fortran programs converted in C by f2c. The cheapest way I have found, efficient for programs not doing graphism but only calculation. Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France http://fluo.univ-lemans.fr:8001/ and/or http://pcb4122.univ-lemans.fr/ From usdccz73@ibmmail.com Mon Nov 25 16:49:33 1996 Received: from ibmmail.COM for usdccz73@ibmmail.com by www.ccl.net (8.8.3/950822.1) id QAA17944; Mon, 25 Nov 1996 16:34:17 -0500 (EST) From: Message-Id: <199611252134.QAA17944@www.ccl.net> Received: from ibmmail by ibmmail.COM (IBM VM SMTP V2R3) with BSMTP id 3644; Mon, 25 Nov 96 10:17:27 EST Date: Mon, 25 Nov 1996 10:16:40 EST To: Chemistry@www.ccl.net Subject: Call for Papers, 29th ACS Central Regional Meeting, Midland, Mich NOTE FROM: C. Peter Qian NITC EXPR CTR CO41B1 Dow Corning Corp. SUBJECT: Call for Papers, 29th ACS Central Regional Meeting, Midland, Mich A symposium titled Computational Tools for Today's Chemist will be held at 29th ACS Central Regional meeting in Midland, Michigan, USA during May 28-30, 1997. The topics include materials properties, drug design and method development using computational chemistry and molecular modeling tools. The organizers would like to focus on how the computational tools contribute to the successful applications in their research and development both in industries and academia. Abstracts with 200 to 300 words in standard ACS abstract format must be received by Friday, January 17, 1997. A standard ACS abstract form can be obtained by calling 1-800-227-5558 or by internet at http://www.acs.org/meetings/abstract/abinfo.html. You may send abstracts to Dr. Tyler B. Thompson by one of the following methods: e-mail acscrm@dow.com or conventional mail: 1801 Building The Dow Chemical Company Midland, MI 48674-1801 The organizers also need one or two invited speakers for this symposium, and welcome volunteers and suggestions about the possible candidate. Please send questions regarding this session to: C. Peter Qian Process Engineering - CO41B1 Dow Corning Corporation Midland, MI 48686 usdccz73@ibmmail.com Tel: (517)496-6938 Fax (517)496-5121 C. Peter Qian NITC EXPR CTR, CO41B1, Dow Corning Corp. Midland, MI 48686-0994 usdccz73@ibmmail.com, Tel. (517)496-6938, Fax (517)496-5121 From polowin@hyper.hyper.com Tue Nov 26 10:06:26 1996 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.8.3/950822.1) id JAA24787; Tue, 26 Nov 1996 09:35:38 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [206.51.24.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id JAA08637; Tue, 26 Nov 1996 09:39:36 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:edanoff@unm.edu id AA18039; Tue, 26 Nov 96 09:39:21 -0500 Date: Tue, 26 Nov 96 09:39:21 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9611261439.AA18039@hyper.hyper.com> To: "Anatoli Korkin" , edanoff@unm.edu Subject: Re: CCL:G:Gaussian 94 Visualization Cc: chemistry@www.ccl.net > From: "Anatoli Korkin" > Date: Mon, 25 Nov 1996 23:30:53 -0500 > > It is easy problem. You do not need a special program, because "newzmat" > (read gaussian manual) can convert your z-matrix into pdb format. Hyperchem > can read it. You only need to change the extention "pdb" into "ent". > For some reasons pdb format files in Hyperchem have the extention "ent". They have that extension because that is the extension used in the Brookhaven Protein Data Bank itself. Your solution will probably work properly, but one must be careful if the structure includes standard PDB residues -- if atoms are missing from standard residues when a PDB file is read, HyperChem will attempt to add the missing atoms, using information from its residue templates. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From ccl@www.ccl.net Tue Nov 26 11:03:25 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA25421; Tue, 26 Nov 1996 10:31:08 -0500 (EST) Received: from wugate.wustl.edu for gregory@ibc.wustl.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA10365; Tue, 26 Nov 1996 10:31:08 -0500 (EST) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id JAA10945; Tue, 26 Nov 1996 09:30:51 -0600 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id JAA23197; Tue, 26 Nov 1996 09:30:47 -0600 Date: Tue, 26 Nov 1996 09:30:46 -0600 (CST) From: Gregory Nikiforovich To: chemistry@ccl.net cc: nobody@net.bio.net Subject: Conformational calculations for peptides Message-ID: Dear all: One of the best approaches to conformational computations of peptides includes combination of a build-up protocol and the ECEPP force field (see Nikiforovich GV (1994) Int.J.Pept.Prot.Res.vol.44,pp. 513-531). For many years, we have developed a technology of calculations using this approach. The main advantages are that the user can handle a bunch of different conformers simultaneously ensuring rather comprehensive yet not random sampling of the conformational space. This technology is implemented in various pieces of software, allowing to select general strategy of build-up protocol in terms of sequences considered (i.e., start from VYVH to VYVHPF to RVYVHPF to DRVYVHPF - angiotensin II) and to push the button starting calculations. The results are the sets of low-energy backbone conformers with optimized spatial arrangements of side chains. We are considering possibility to assemble these various pieces into a single automatic program running under various computer systems, and to make it accessible to others. Now the question: would anybody be interested in such program? We do not want to waste our time and money on the "non-marketable" project. Thank you in advance for your response. Please e-mail it directly to my e-mail address. Your response will really help us. Gregory V. Nikiforovich Research Professor Phone (314) 362-1566 Center for Molecular Design FAX (314) 362-0234 Washington University E-mail address: Institute for Biomedical Computing gregory@ibc.wustl.edu Box 8036, 700 South Euclid Ave. St. Louis, MO 63110 From ccl@www.ccl.net Tue Nov 26 17:49:30 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id RAA28872; Tue, 26 Nov 1996 17:00:25 -0500 (EST) Received: from tlon.unq.edu.ar for seba@tlon.unq.edu.ar by bedrock.ccl.net (8.8.3/950822.1) id RAA21091; Tue, 26 Nov 1996 17:00:22 -0500 (EST) Received: from alien.unq.edu.ar (alien10.unq.edu.ar [170.210.73.80]) by tlon.unq.edu.ar (8.8.3/8.8.3) with SMTP id TAA03473 for ; Tue, 26 Nov 1996 19:03:26 -0300 Date: Tue, 26 Nov 1996 19:03:26 -0300 Message-Id: <199611262203.TAA03473@tlon.unq.edu.ar> X-Sender: seba@tlon.unq.edu.ar X-Mailer: Windows Eudora Versión 1.4.4 To: chemistry@ccl.net From: seba@tlon.unq.edu.ar (sebastian fernandez) Subject: telaxation time of ACF for methanol and acetone Dear Srs. Does anybody know the relaxation times of velocities autocorrelation functions of the center of mass for pure methanol and pure acetone? Thanks in advance. Sebastian Fernandez Alberti Centro de Estudios e Investigaciones Univ. Nacional de Quilmes Saenz Pena 180, 1876 Bernal, Prov. Buenos Aires Argentina From ccl@www.ccl.net Wed Nov 27 01:09:42 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id AAA00589; Wed, 27 Nov 1996 00:45:59 -0500 (EST) Received: from curie.syr.edu for cmartin@curie.syr.edu by bedrock.ccl.net (8.8.3/950822.1) id AAA26338; Wed, 27 Nov 1996 00:45:58 -0500 (EST) Received: by curie.syr.edu (950413.SGI.8.6.12/940406.SGI.AUTO) id AAA24313; Wed, 27 Nov 1996 00:27:10 -0800 Date: Wed, 27 Nov 1996 00:27:10 -0800 Message-Id: <199611270827.AAA24313@curie.syr.edu> From: Charles Martin To: chemistry@ccl.net Subject: Anion basis sets for excited state calculations Hello Netters, I am running ab initio excited state calculations on phenolate [Bz-O(-)] and some larger, conjugated phenolate derivatives. I am hoping that someone has some experience in choosing the proper ab initio basis set (i.e. do I need special functions for the O- non-bonding orbitals) and the selection of the LUMO orbitals for a correlated, multi-reference configuration calculation. I have seen only 1 recent Bz-O(-) calculations using the CASPT2 method, but the details are scarce. Perhaps some of you have performed CASPT2, MRSDCI, EOM-type, etc., calculations on negative ions of this type and have some experience that you could share with me? Thanks in advance Chuck Martin -- ======================================================== || Charles H. Martin || || 2-004 Center for Science and Technology || || W. M. Keck Center for Molecular Electronics || || Department of Chemistry || || Syracuse University || || Syracuse, NY 13244 || -------------------------------------------------------- || cmartin@cat.syr.edu || || cmartin@rainbow.uchicago.edu || || OFFICE (315) 443-3754 || || LAB (315) 443-5928 || || FAX (315) 443-4070 || ======================================================== From ccl@www.ccl.net Wed Nov 27 10:54:33 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA03167; Wed, 27 Nov 1996 09:50:37 -0500 (EST) Received: from rune.biokemi.su.se for arne@rune.biokemi.su.se by bedrock.ccl.net (8.8.3/950822.1) id JAA01273; Wed, 27 Nov 1996 09:50:35 -0500 (EST) Received: (from arne@localhost) by rune.biokemi.su.se (8.7/8.7) id PAA28353; Wed, 27 Nov 1996 15:50:11 +0100 (MET) To: Tore.Samuelsson@medmod.medkem.gu.se, CHEMISTRY@ccl.net Subject: bioinformatics on the Internet From: Arne Elofsson Date: 27 Nov 1996 15:50:11 +0100 Message-ID: Lines: 80 X-Mailer: Gnus v5.2.37/XEmacs 19.14 Dear ..... Recently I taught a course in "bioinformatics on the Internet", and I thought that my experiences could be important to others too. All information about the course including assignments etc can be found at http://www.biokemi.su.se/~arne/kurser/kurs_96/ The course was given to about 20 students with very different backgrounds. This was of course a problem. The computer scientists and the physicists was much easier to teach than the biochemists and molecular biologists. The main problems for the bio-students were to get programs such as rasmol to work on their Mac's without crashing too often etc. (Is this possible ?) Further I was the only teacher, except for about 9 guest lecturers, this made it impossible to organize computer labs etc. Therefore all assignments was supposed to be done by the students them self, without any supervision. This proved to work fine for the computer/physics students while it took a lot of time for the bio-student to get everything running. Please feel free to read the http pages and if anyone has any input I would really appreciate that. OK, so what did I learn. General ------- 1) Computer demonstrations/labs should be given in first week I think this is necessary and actually will save time, as the students then at least know how to use netscape and rasmol. 2) Use more interactive lectures (do the assignments) It is more fun, but take more time to prepare, and I would have to use a MAC. Well I could probably run Linux on a PC so that is OK. 5) Local servers for something to speed up things. Some servers are very slow, therefore it could be a good idea to set up some servers (like blast) locally. Problems -------- 1) UCLA threader server The organizer refused to give my students access to their threading page. 2) Slow responds from some servers sometimes For instance PHD sometime took several days to answer. 3) My local alignment page needs to be improved 4) Very low interaction on the net between students This is to bad, I do not know hoe to improve that. Mailing lists is the only alternative as no bio-students read news or surf regularly. Maybe I should set up some assignments where it is necessary to collaborate with each other. but HOW ? thanxs arne -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@bimbo.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From MAILER-DAEMON@www.ccl.net Thu Nov 28 15:49:52 1996 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA13014; Thu, 28 Nov 1996 15:23:27 -0500 (EST) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id VAA18233; Thu, 28 Nov 1996 21:23:10 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9611282123.ZM18231@eros.ccc.uni-erlangen.de> Date: Thu, 28 Nov 1996 21:23:06 +0100 In-Reply-To: iguana@one.net (Ray Crawford) "CCL:Formula names from SMILES" (Nov 28, 10:55) References: <199611281555.KAA08038@one.net> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: iguana@one.net (Ray Crawford) Subject: Re: CCL:Formula names from SMILES Cc: chemistry@www.ccl.net On Nov 28, 10:55, Ray Crawford wrote: > Subject: CCL:Formula names from SMILES > Howdy!! > > I was wondering if anyone out there knows of a program (or script) > that converts Daylight SMILES to molecular formulas... I was getting ready > to write my own script in PERL but decided to ask before dedicating a few > hours to the task... Assuming that your want something like 'C3H8' from SMILES string 'CCC': Get the CACTVS tools (http://schiele.organik.uni-erlangen.de/cactvs). The structure editor (csed) can convert SMILES to structures and will also display the formula. For batch processing, write a script for the GUI-less 'tclserver' program in the package: (reads from stdin, writes to stdout) #!/usr/local/bin/tclserver while 1 { set smiles [gets] if {$smiles==""} exit set ehandle [ens create $smiles] puts [ens get $ehandle E_FORMULA] ens delete $ehandle } -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From ccl@www.ccl.net Fri Nov 29 13:16:09 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA18092; Fri, 29 Nov 1996 12:28:49 -0500 (EST) Received: from occam.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by bedrock.ccl.net (8.8.3/950822.1) id MAA21402; Fri, 29 Nov 1996 12:28:45 -0500 (EST) Received: from localhost (craig@localhost) by occam.gh.wits.ac.za (8.7.5/8.7.3) with SMTP id TAA20563; Fri, 29 Nov 1996 19:11:26 +0200 X-Authentication-Warning: occam.gh.wits.ac.za: craig owned process doing -bs Date: Fri, 29 Nov 1996 19:11:26 +0200 (SAT) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Chemistry lists for indaba mail shot , chem-mod@mailbase.ac.uk, chemconf@umdd.umd.edu, chemed-l@uwf.cc.uwf.edu, chemic-l@taunivm.tau.ac.il, computational chemistry , chemweb@ic.ac.uk, Small Molecules Indaba II , mmodinfo@uoft02.utoledo.edu, mmodlist@chem.iupui.edu, mol-diversity@listserv.arizona.edu, watoc@ic.ac.uk Subject: Intermolecular Interactions - Structural Chemistry Indaba II Message-ID: STRUCTURAL CHEMISTRY INDABA II - INTERMOLECULAR INTERACTIONS FIRST ANNOUNCEMENT AND CALL FOR CONTRIBUTIONS This posting is being sent to a number of mail lists, and we appologise in advance if you receive it more than once. Please could you inform any potentially interested collegues and students of this conference announcement, and, if possible, post it on any relevant departmental noticeboards. One page postscript versions are available on request. We also welcome any interest from students and young scientists. The information contained below is a copy of the information on the conference WWW page: http://www.gh.wits.ac.za/indaba The WWW page should be considered the definitive source, and will be updated regularly. Pre-registration and booking of accomodation places can be achieved with the registration form: http://www.gh.wits.ac.za/indaba/reg-indaba.html Any emails should be directed to "indaba-org@hobbes.gh.wits.ac.za". Yours Sincerely, The Organizing Committee **************************************************************************** Contents: [Theme] [Invited Lecturers] [Venue] [Cost] [Transport] [Accommodation] [Registration] [Contacts] **************************************************************************** Due to the success of the First Small-molecules Indaba, this second Indaba is being planned for 3rd to the 8th August 1997. Structural Chemistry Indaba II 3-8 August 1997 Intermolecular Interactions **************************************************************************** An international workshop organized by the South African Crystallographic Society in collaboration with the Commission on Structural Chemistry of the International Union of Crystallography. IUCr Scientific Freedom Policy Statement: The Organising Committee of the Structural Chemistry Indaba shall observe the basic policy of non discrimination and affirms the rights of scientists throughout the world to adhere to or to associate with international scientific activity without restrictions based on nationality, race, colour, age, religion, political philosophy, ethnic origin, citizenship, language, or sex, in accordance with the Statutes of the International Council of Scientific Unions. At this conference no barriers will exist which would prevent the participation of bona fide scientists. Indaba is an African term to describe a meeting to analyze a difficult problem from all angles **************************************************************************** Theme - Intermolecular Interactions Each of the invited lecturers will address a different aspect around the central theme of Intermolecular Interactions, starting with a critical overview of the assumptions common amongst structural chemists. The idea of intermolecular interactions relates to the notion that materials in the bulk consist of weakly interacting units, or molecules, in the sense that intramolecular interactions are stronger than these, by orders of magnitude. In view of this it is argued that, by ignoring the weak interactions, the same molecular units that occur in the gas phase can be recognized in condensed phases. At the same time it is commonly accepted that solid materials exhibit many properties not apparent in other phases and acquired as a result of intermolecular interactions only. From both points of view the concept is rather ill-defined and of questionable importance. The problem relates to the model of choice to describe condensed phases. Defined as single quantum-mechanical systems there is no basis to distinguish between intra- and intermolecular forces. An intermolecular interaction is then defined only for the gas phase, where it is practically negligible in any case. An attempt to distinguish between intra- and intermolecular interactions necessarily fails to recognize their interdependence and creates artifacts to be used later on as independent concepts, in terms of which to explain chemical behavior. In terms of deformation electron densities in crystals the distinction becomes even more vague and the definition of molecular units even more arbitrary. Answers to these questions are probably not simple and different points of view can surely be formulated in all cases. In this sense it provides a worthy topic for discussion at a special symposium in the spirit of the 1995 Small-molecules Indaba. **************************************************************************** Invited Lecturers Note: This is a preliminary list. Some still have to be confirmed and one or two more lecturers may still be invited. Name From Topic F.H.Allen Cambridge, UK The relationship between theory and experiment in the study of non-covalent interactions. A.Amann ETH, Switzerland The shape of interacting molecules I.Bernal Houston, USA Conglomerate Crystallization. J.C.A.Boeyens Witwatersrand, Intermolecular Bonding South Africa D.Braga Bologna, Italy Supramolecular organization in organometallic crystals. P.Comba Heidelberg, Intermolecular effects in Germany coordination chemistry. T.Cundari Memphis, USA Modeling intermolecular effects G.Gilli Ferrara, Italy Strong interactions (or incipient interactions) in molecular crystals: an implicit criticism of the inter-intramolecular dichotomy. J.A.K.Howard Durham, UK Intermolecular effects at 10K. C.Krueger MPI, Germany Electron deformation densities. T.Koritsanszky Berlin, Germany Electron densities between molecules. P.Luger Berlin, Germany Interactions at low temperatures. J.Ogilvie Oregon, USA Dynamic aspects of intermolecular interactions. A.G.Orpen Bristol, UK Structural evidence of intermolecular interactions. E.Osawa Japan Design of Crystal Properties. D.Rouvray UK Fuzzy logic applied to the molecular sphere. B.T.Sutcliffe York, UK Molecular properties in different environments. **************************************************************************** Venue As with the Conference in August 1995, the second Indaba will be held in one of the most famous national parks in the world and the oldest one in Africa, the Kruger National Park. The same venue as before, the picturesque Skukuza camp, has been secured for the duration of the workshop. One of the Park's main objectives is to maintain the ecosystem in its natural state and to offer the visitor an unrivaled experience of African wildlife. While offering excellent accommodation facilities, the Park has retained a genuine African atmosphere - to the delight of the scores of visitors to the New South Africa. The Climate is subtropical, with days normally sunny, warm and clear. During August, just before the onset of the warm African summer, the temperatures are moderate and pleasant. In this regard the South African author and nature lover, C Louis Leipoldt, wrote: "The ideal time to visit the Bushveld is in winter, from May to November. Then the climate is charmingly even: its mornings, when the sun tinges the tops of the bush, are delightfully crisp and cool; its noon is pleasantly but not relaxingly warm; its afternoons and evenings, stained by an all-too-brief afterglow with amazingly vivid colouring, are as mild and beautiful as a summer's night in Europe". Excursions into the Park will give both delegates and accompanying persons many opportunities to view the unparalleled diversity of wildlife, including antelope, buffalo, elephant, lion, leopard, cheetah, wild dog, hyena, jackal, black and white rhinoceros, an exceptional variety of bird species and numerous other wild creatures. Skukuza is the Kruger Park's main camp. Dress code: Casual. **************************************************************************** Cost Final Pricing Registration fee includes admittance to all scientific sessions, the Book of Abstracts, the meet and greet party on Sunday, the traditional $330 braai, a daily finger buffet breakfast and teas, as well as daily excursions into the park Early registration payment must be received before April 15, 1997 $280 Student registration For subsidised students $100 Accompanying persons registration fee includes only the traditional braai and daily excursions into $100 the park Transport between the airport and Skukuza camp includes entrance fee into Kruger Park $100 Banquet a traditional dinner to be held on Tuesday 5th $30 Note: * The above costs do NOT include accommodation costs nor meals not explicitly included above. * The daily finger breakfast buffet will be provided at the lecture hall, as will the teas. * The camp has restaurant facilities for normal meals, breakfast, lunch and supper, with prices ranging from $5 to $12. * People making their own way to the park will have to pay for the park entrance at the gate (about $15 per car and $4 per person).. * PLEASE NOTE: The number of participants is restricted due to limitations in accommodation at Skukuza camp. PLEASE BOOK EARLY. **************************************************************************** Transport International Johannesburg International Airport is well utilized by many major airlines from Europe, America and most other parts of the world. Normally trips from Europe last over 12 hours and are undertaken overnight, so leaving on the evening of Saturday the 2nd of August will allow you to arrive at JIA on Sunday the 3rd. Flights leaving JIA on the evening of Friday 8th August will arrive in Europe on the morning of Saturday 9th. Travelers from Europe will feel no jet lag, but the Americas are 6 to 9 hours behind South Africa, while Asia is 2 to 10 hours ahead. Visas may be required for some countries. Please make all travel arrangements with your local travel agents, but inform us of your arrival date, time, flight number etc. Coach Transport from the airport to the Skukuza camp in the Kruger National Park will be provided by coach for those that require it, at a cost of $100 per person. The bus trip will include refreshments and orientation information. For accompanying persons, and conference attendees, the bus will remain available for daily excursions into the park for the duration of the conference. The use of the bus for these excursions is included in the registration fee. The full bus fare is for the trips to and from the airport on the 3rd and 8th. Preliminary dates are: JIA to Skukuza morning of 3rd August Park outings afternoons of 3rd to 7th August Skukuza to JIA afternoon of 8th August Car Rental Many international car rental companies (Avis, Hertz, Bugdget, etc.) are represented in South Africa. Attendees wishing to rent cars should apply through their local travel agents. **************************************************************************** Accommodation Accommodation available at Skukuza camp is in typical national park style. The rondawels are individual huts with hot and cold running water, linen service, and full ablution facilities. The number of beds per rondawel ranges from 2 to 6. To facilitate bookings the accommodation has been grouped into three categories. The following prices are per person per night: category price pp pn deposit luxury (single) $60.00 $150.00 standard (sharing) $30.00 $75.00 basic (sharing) $25.00 $65.00 * Please indicate your order of preference on the registration form * Families or groups wishing to stay together must contact us well in advance to ensure booking of appropriate accommodation. Prices for such arrangements will depend on final availability. * Because the accommodation capacity within each category varies, it is impossible to guarantee a specific allocation. We will, however, try our best to meet your specific requirements. * Accommodation will be allocated on a first come, first served basis. * For shared accommodation, please indicate any partner preferences. * The required deposit must be received by 31st June 1997 and will contribute towards the full accommodation cost, the balance of which can be settled on arrival. **************************************************************************** Registration and Submission of Abstracts Deadlines early bird registration 15th April 1997 final registration 15 June 1997 final payments due 31 June 1997 submission of abstracts 31 June 1997 Cancellation Penalties before 31st July 50% after 31st July no refund Registration A registration form is available on the WWW at http://www.gh.wits.ac.za/indaba/reg-indaba.html. This form can be used for preliminary registration to book a place at the indaba. If you would prefer to fax the registration form, you may do so by either printing the WWW page, or by using the text only page at http://www.gh.wits.ac.za/indaba/reg-indaba.txt. This text only page is also ideal for emailing your registration to the primary contact email address below. Payment There are two preferred methods of payment 1. Direct bank transfer into the bank account: "Structural Chemistry Indaba" Account number 1951076273 NedBank, Johannesburg,Wits branch 19510502 SOUTH AFRICA 2. Cheque or bank draft made payable to the above account and mailed to the primary registration mail address below. Please also contact us via email, fax or mail when you make the transfer, so that we have our own record of the payments. If you would prefer to pay with a credit card, arrangements can be made, but a surcharge of 6% will be charged. Submission of Abstracts Submission of abstracts can be made by mail, email or ftp. If using mail or email, please post to the primary contact address below. If using ftp please ftp into the anonymous ftp account at ftp://www.gh.wits.ac.za/indaba. Electronic submission of abstracts will be accepted in the following formats only: * plain text (ASCII) * postscript * TeX and LaTeX * WP5.1 and WP6.0 for DOS or Windows (not Macintosh) * Word2.0 for Windows (not Macintosh) All these formats will be accepted for ftp submissions. For email submissions, the plain text, TeX, LaTeX and postscript files can be sent in the body of the email or as attachments, while the WP and Word files must be sent as attachments. apologies, but Macintosh attachments can NOT be accepted. If you are using a Macintosh email program, please only use the text formats (plain text, postscript, TeX or LaTeX) and include the submission in the body of the mail. Note that since the number of participants will be limited, and interest in the conference is high, early registration is very advisable. **************************************************************************** Contacts The primary means of contacting the organizers for information, registration, and submission of abstracts will be through the e-mail address: indaba-org@hobbes.gh.wits.ac.za . This address is guaranteed to reach the person most likely to be in a position to answer any questions you might have, or provide the information you are looking for. The primary telephone, fax and mail address for submission of registration, abstracts and payment by cheque or bank draft is: Lesley Stephenson Structural Chemistry Indaba tel: +27-11-716-5091 CEE Conference Office s-mail: PO Box 327 Wits University WITS 2050 fax: +27-11-716-7835 South Africa If you specifically wish to contact individuals, use the following contact details: Programme Committee Chairman Organizing Committee Chairman e-mail: Prof. Jan Boeyens e-mail: Dr. Demi Levendis jan@hobbes.gh.wits.ac.za demi@hobbes.gh.wits.ac.za Prof. Jan Boeyens Dr. Demi Levendis Structural Chemistry Indaba Structural Chemistry Indaba Chemistry Department Chemistry Department s-mail: Private Bag 3 s-mail: Private Bag 3 Wits University Wits University WITS 2050 WITS 2050 South Africa South Africa tel: +27-11-716-4097 tel: +27-11-716-2348 fax: +27-11-716-3826 fax: +27-11-716-3826 Conference Organizers Internet and Communications e-mail: Lesley Stephenson e-mail: Craig Taverner Stephenson@egoli.min.wits.ac.za craig@hobbes.gh.wits.ac.za Lesley Stephenson Craig Taverner Structural Chemistry Indaba Structural Chemistry Indaba CEE Conference Office Chemistry Department s-mail: PO Box 327 s-mail: Private Bag 3 Wits University Wits University WITS 2050 WITS 2050 South Africa South Africa tel: +27-11-716-5091 tel: +27-11-716-2290 fax: +27-11-716-7835 fax: +27-11-716-3826 **************************************************************************** last change 29/11/96 This site is maintained by Craig Taverner (craig@hobbes.gh.wits.ac.za) **************************************************************************** **************************************************************************** From arthur@csb0.IPC.PKU.EDU.CN Fri Nov 29 21:50:07 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id VAA19311; Fri, 29 Nov 1996 21:30:10 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA27200; Sat, 30 Nov 96 10:29:38 -0800 Date: Sat, 30 Nov 1996 10:29:36 -0800 (PST) From: Arthur Wang To: CCL mailing list Cc: Structrual Biology List Subject: Summary: Free databases for small molecules Message-Id: Dear Netters, About a weeks ago, I put forward the question "Where to find free databases on-line for small molecules". Now I have collected many answers as listed below. Here we thank all the netters who have contributed. ------------------------------------------------------------------------ From: DOUGH@mdli.com You can find a 33 Mb compressed MDL SDfile format file of the NCI-3D database (126K structures) at ftp://helix.nih.gov/ncidata/3D/ You should read the nciopen3d.readme file there, and, I'm not sure if it's available to just anyone. I didnt try downloading it. My understanding is that these are structures submitted to NCI for testing, which have been released for public access. Companies like Daylight, MDLI, and Tripos have also made these structures available as part of their database systems. You would need either to put the structures into a database (e.g., depending on the size of your PC, ISIS/Base could be used - may have to create a few subset databases), or devise a means of extracting the desired molfiles from the sdfile. The MDLI homepage has a link to a description of the MDL Mol and SDfile formats, which are quite simple. ----------------------------------------------------------------------- From: aumelas@auvergne.cbs.univ-montp1.fr (Andre Aumelas) Dear Arthur, You can get stuctures of small molecule at http://www.ibc.wustl.edu/klotho Andre Aumelas ------------------------------------------------------------------------ From: "N.Ganesh" dear arthur you could get the cambridge database listings from Stan Cameron (EMAIL: CAMERON@ac.dal.ca).This is for nucleotides and nucleotides,but i am not to sure whether it is available free or whether one has to pay for it regards ganesh ------------------------------------------------------------------------ From: (Chemical Physics Institute) Dear Arthur, try http://www.csc.fi/lul/rtam/ with large database on relativistic compounds. You may also try some sites where there is a lot of chemical info, like http://hackberry.chem.niu.edu ------------------------------------------------------------------------- From: Richard Gillilan Check out this page, for example: http://epnws1.ncifcrf.gov:2345/dis3d/3Ddatabase/dis3d.html ------------------------------------------------------------------------- From: jsb2@camsoft.com To the best of our knowledge, the ChemFinder WebServer (http://chemfinder.camsoft.com) is the largest substructure-searchable chemical database on the Internet, with over 20,000 entries at the moment. Jonathan Brecher -------------------------------------------------------------------------- From: Csonka Gabor Dear Arthur Wang, recently I have collected some useful structural databases. You can visit: http://web.inc.bme.hu/~csonka/mke96.html I suggest ChemFinder. -------------------------------------------------------------------------- From: Shu-Kun Lin Dear Dr. Wang: MDPI is the source. Please visit http://www.mdpi.org/ Shu-Kun Lin -------------------------THE END------------------------------------------ Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From Eugenia.Migliavacca@ict.unil.ch Mon Dec 2 05:50:38 1996 Received: from unilmta3.unil.ch for Eugenia.Migliavacca@ict.unil.ch by www.ccl.net (8.8.3/950822.1) id FAA02417; Mon, 2 Dec 1996 05:16:15 -0500 (EST) Message-Id: <199612021016.FAA02417@www.ccl.net> Received: from pcbep5005c.unil.ch by unilmta3.unil.ch with SMTP inbound; Mon, 2 Dec 1996 11:15:46 +0100 X-Sender: emigliav@ulys.unil.ch X-Mailer: Windows Eudora Version 2.1.1 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 02 Dec 1996 11:18:11 +0100 To: Computational Chemistry Mailing List From: Jenny Subject: Summary:radical cations in solution Dear CCLers, I thank Alan Shusterman and Christopher J. Cramer for the very useful advices. Some days ago, I submitted the following question: >Date: Wed, 27 Nov 1996 19:05:25 +0100 >To: Computational Chemistry Mailing List >From: Jenny >Subject: radical cations in solution > >Dear CCLers, > >I am interested in the calculation of minimum energy conformations of a radical cation (17 heavy atom: C, O, N) in solution (water). >Can continuum solvation models be used to investigate geometries and relative energies of different conformers? >Is AMSOL a good choice? > >Please, reply directly to me (Eugenia.Migliavacca@ict.unil.ch). I will summarize the answers for the CCL. > >Thank you in advance >and best regards, > >Jenny > first reply >Date: 27 Nov 96 15:16:07 PST >From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) >Subject: Re: CCL:radical cations in solution >To: Eugenia.Migliavacca@ict.unil.ch > >The answer is definitely "maybe". HF models of delocalized radical cations are >problematic. One typically uses UHF wavefunctions to describe open shell >species, and a good argument can be made that UHF wavefunctions are inherently >unsuitable for delocalized radical cations (see P.C. Hiberty, S. Humbel, D. >Danovich and S. Shaik, "What Is Physically Wrong with the Description of >Odd-Electron Bonding by Hartree-Fock Theory? A Simple Nonempirical Remedy", >J.Am. Chem. Soc., 1995, 117, 9003-9011). > >Of course, there are other ways to get reasonable electronic descriptions of >radical cations, but I can't tell you if coupling these models with continuum >solvation models makes sense. Good luck. > >Alan Shusterman >Department of Chemistry >Reed College >Portland, OR 97202 second reply >From: Christopher J Cramer >Subject: Re: CCL:radical cations in solution >To: Eugenia.Migliavacca@ict.unil.ch (Jenny) >Date: Wed, 27 Nov 1996 21:39:33 -0600 (CST) >Content-Length: 1153 > > AMSOL will certainly do the calculations, but one needs to be aware that >(i) solvation free energies for charged species can have substantial errors >(say 5 kcal/mol) because they are typically large in magnitude and for other >reasons. Conformational analysis would require cancellation of errors. (ii) >The AMSOL solvation free energies will be more trustworthy than the AM1 or >PM3 conformational energies. We typically construct hybrid energies from good >ab initio theory plus SMx solvation free energies (assuming solvation effects >on geometries are small -- not always a good assumption). > >Chris > >Christopher J. Cramer >University of Minnesota >Department of Chemistry >207 Pleasant St. SE >Minneapolis, MN 55455-0431 >-------------------------- >Phone: (612) 624-0859 || FAX: (612) 626-7541 >cramer@maroon.tc.umn.edu >http://pollux.chem.umn.edu/~cramer Jenny Migliavacca Institut de Chimie Therapeutique Ecole de Pharmacie Universite de Lausanne CH-1015 Dorigny-Lausanne Tel: 021 / 692.45.29 Fax: 021 / 692.45.05 Email: Eugenia.Migliavacca@ict.unil.ch From LIN@ubaclu.unibas.ch Mon Dec 2 06:50:41 1996 Received: from swiba9.unibas.ch for LIN@ubaclu.unibas.ch by www.ccl.net (8.8.3/950822.1) id GAA02676; Mon, 2 Dec 1996 06:23:33 -0500 (EST) Received: from yogi.urz.unibas.ch by swiba9.unibas.ch with SMTP (PP); Mon, 2 Dec 1996 12:21:34 +0100 Received: from ubaclu.unibas.ch by ubaclu.unibas.ch (PMDF V4.3-7 #7496) id <01ICJ8RP19IO938JA2@ubaclu.unibas.ch>; Mon, 2 Dec 1996 12:21:11 +0100 Date: Mon, 02 Dec 1996 12:17:12 +0100 From: Shu-Kun Lin Subject: Summary IUPAC names from structure files To: chemistry@www.ccl.net Message-id: <01ICJ8XGE08K938JA2@ubaclu.unibas.ch> Organization: University of Basel, Switzerland MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT On Nov 27, 3:21pm, Shu-Kun Lin wrote: > Subject: CCL:IUPAC name > Dear Colleagues: > Where can I get a software for me to generate IUPAC names if > I have 2D structures or Daylight SMILES or MDL MolFiles? Reply 1: http://www.acdlabs.com from: Victor S. Lobanov, PhD 3-Dimensional Pharmaceuticals, Inc. e-mail: victor@3dp.com 665 Stockton Drive, Suite 104 tel: (610) 458-8959 Exton, PA 19341 fax: (610) 458-8249 ------------------------------------------------------------------------------ Reply 2: IMHO this is a very important subject, please make a summary, or mail me the best infos you get. Many greetings from Bavaria Ralph Puchta (Puchta@GWUP.org) ------------------------------------------------------------------------------ Reply 3: as far as I know there are only two programs for generating IUPAC-names from structure files. There is Autonom from Beilstein and ACD/name from ACD. Unfortunatly I don't know which kind of structure files these programs support, but perhaps you get more information from their web pages: http://pubs.acs.org/pin/acd/acindex.html http://www.beilstein.com From: Thomas Kostka Computer-Chemie-Centrum, Univ. Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6578 Fax (+49)-(0)9131-85-6566 Email: kostka@torvs.ccc.uni-erlangen.de ____________________________________________________ Reply 4: I know about two products: AUTONOM (Beilstein Information Systems) and ACD/Name (ACDlabs, see http://www.acdlabs.com/products/name/name_predict_clip.htm From: Dr. Wolf-Dietrich Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 ____________________________________________________ Concluding Remarks: Software like Chem/Draw or ISIS/Draw or database software like Daylight and ISIS/Base may include such function into their software. Once a correct structure is prepared, an IUPAC name should be automatically generated, like so far automatically produced molecular formula (e.g., C10H20N5) and molecular weight (e.g., 345.67) from a structure in these software packages. Thanks! Shu-Kun --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland MDPI: http://www.mdpi.org/ Molecules: http://science.springer.de/molec/molecule.htm e-mail: LIN@ubaclu.unibas.ch Lin@mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- From anthony.debellis@ustc.MHS.CIBA.COM Mon Dec 2 10:50:43 1996 Received: from gatekeeper.chbs.ciba.com for anthony.debellis@ustc.MHS.CIBA.COM by www.ccl.net (8.8.3/950822.1) id KAA03792; Mon, 2 Dec 1996 10:22:26 -0500 (EST) Received: from cgchm.is.chbs by gatekeeper.chbs.ciba.com; (5.65v3.2/1.1.8.2/12Mar96-0208PM) id AA30094; Mon, 2 Dec 1996 16:27:36 +0100 Received: from mta1.is.chbs by Central.CHBS.CIBA.COM id AA17778; Mon, 2 Dec 1996 16:21:54 +0100 (5.65c8/Ciba2.0-C1.1) Received: by mta1.is.chbs (5.65v3.2/DEC-Ultrix/4.3) id AA03127; Mon, 2 Dec 1996 16:21:02 +0100 X400-Received: by mta chbs-mta1 in /PRMD=ciba/ADMD=attmail/C=ch/; converted ((1) (0) (10021) (7) (1) (0) (1), (1) (0) (10021) (7) (1) (0) (6)); Relayed; 2 Dec 1996 15:21:01 +0000 X400-Received: by /PRMD=CIBA/ADMD=ATTMAIL/C=CH/; converted ((1) (0) (10021) (7) (1) (0) (1), (1) (0) (10021) (7) (1) (0) (6)); Relayed; 2 Dec 1996 10:16:39 +0500 Date: 2 Dec 1996 10:16:39 +0500 X400-Originator: anthony.debellis@usgr-msm3.ustc.mhs.ciba.com X400-Mts-Identifier: [/PRMD=CIBA/ADMD=ATTMAIL/C=CH/;961202051639] From: "Debellis,Anthony MSM TCAD US" To: "'Comp Chem List Post'" Subject: RE: vibration coordinates Importance: normal Autoforwarded: FALSE Message-Id: <"0008DACE.MAI*/PN=anthony.debellis/OU=usgr-msm3/OU=ustc/O=ciba/PRMD=CIBA/ADMD=ATTMAIL/C=CH/"@MHS> Original-Encoded-Information-Types: (2) (6) (3) (4) (11) Content-Identifier: CSI NC V3.0 X400-Content-Type: P2-1988 (22) Priority: normal >Dear natters, > >I need to get the movements of the different vibrations >in the internal coordinates representation. >Gaussian 94 gives me the movements in the cartesian >coordinates. > >Does anyone know how can I get the vibrations in internal >coordinates representation from Gaussian 94. > >Thanks in advance > >Avital ------------------------------------------------ According the "Exploring Chemistry with Electronic Structure Methods" (2nd edition), Gaussian 94 will print out the displacements for the normal modes in terms of the internal coordinates. They will be labeled as eigenvectors of the Hessian in the output file. See page 74 of the book. Anthony anthony.debellis@ustc.mhs.ciba.com From kotelyan@che.udel.edu Mon Dec 2 12:50:43 1996 Received: from che.udel.edu for kotelyan@che.udel.edu by www.ccl.net (8.8.3/950822.1) id MAA04937; Mon, 2 Dec 1996 12:27:48 -0500 (EST) Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA55833; Mon, 2 Dec 1996 12:27:31 -0500 Date: Mon, 2 Dec 1996 12:27:07 +22305133 (EST) From: Michael Kotelyanskii Sender: Michael Kotelyanskii Reply-To: Michael Kotelyanskii Subject: Re: CCL:polymer journals for computational work To: "Douglas A. Smith Ph.D." Cc: CHEMISTRY@www.ccl.net In-Reply-To: <199611291804.NAA29572@home.CTCnet.Net> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear Doug, First thing I would try if you want to reach polymer community - Macromolecules they publish many polymer related computer simulations, Also German journal Macromolecular Chemistry (Makromolekulare Chemie) Theory and Simulations, (they publish in English) also J.Chem.Phys. and J.Phys. Chem Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 On Fri, 29 Nov 1996, Douglas A. Smith Ph.D. wrote: > What (specifically) polymer journals are read by and published in by > scientists and engineers doing computational work on polymeric systems? > Please give as much detail as you like, and send directly to me. I will > summarize for the net. > > Doug > -- > Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 > The DASGroup, Inc. | fax: (814) 255-3517 > 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com > Johnstown, PA 15905 | WWW: http://www.dasgroup.com > > Contract R&D specialists in modeling, simulation, synthesis and risk > assessment for chemistry, materials science, and biotechnology. > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: dsmith@CTCnet.Net > -- Original Sender From: Address: dsmith@CTCnet.Net > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From rossi@watson.ibm.com Mon Dec 2 13:50:43 1996 Received: from igw3.watson.ibm.com for rossi@watson.ibm.com by www.ccl.net (8.8.3/950822.1) id NAA06109; Mon, 2 Dec 1996 13:28:47 -0500 (EST) Received: from mailhub1.watson.ibm.com (mailhub1.watson.ibm.com [9.2.249.31]) by igw3.watson.ibm.com (8.7.6/8.7.1) with ESMTP id NAA09630 for ; Mon, 2 Dec 1996 13:29:13 -0500 Received: from deus-ex-machina.watson.ibm.com (deus-ex-machina.watson.ibm.com [9.2.201.24]) by mailhub1.watson.ibm.com (8.8.2/11-26-96) with SMTP id NAA582787 for ; Mon, 2 Dec 1996 13:28:47 -0500 Received: from localhost by deus-ex-machina.watson.ibm.com (AIX 4.1/UCB 5.64/6/25/96) id AA28812; Mon, 2 Dec 1996 13:28:47 -0500 Sender: rossi@watson.ibm.com Message-Id: <32A31FDE.41C6@watson.ibm.com> Date: Mon, 02 Dec 1996 13:28:46 -0500 From: Angelo Rossi X-Mailer: Mozilla 3.0 (X11; I; AIX 1) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Student Exercise on Protein Structure and Conformation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello: I am interested in developing an exercise for students relating to protein structure and conformation. Specifically, a molecular modeling package will be used to investigate the primary, secondary and tertiary structure of proteins. Hydrophilicity and hydorphobicity will aslo be dicusssed and related to the types of side chains present. Would those of you who have already formulated exercises like this or can point to references, please send me e-mail directly? Thanks for your help with this. I will summarize for the list. Regards, A. R. Rossi From xavier@stark.udg.es Mon Dec 2 15:50:45 1996 Received: from stark.udg.es for xavier@stark.udg.es by www.ccl.net (8.8.3/950822.1) id OAA06612; Mon, 2 Dec 1996 14:55:30 -0500 (EST) Received: from quantum.udg.es by stark.udg.es via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA00392; Mon, 2 Dec 96 20:58:21 -0800 Message-Id: <9612030458.AA00392@stark.udg.es> X-Sender: xavier@stark.udg.es X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 02 Dec 1996 20:48:03 +0000 To: chemistry@www.ccl.net From: Xavier Subject: 3rd derivatives >Date: Mon, 2 Dec 96 20:48:08 -0800 >From: josepm (Josep Maria Luis Luis) >Apparently-To: xavier > >On Friday, 22 Nov 1996, I posted the following question: > > Dear CCLers, > I am interested in computing analytical energy third derivatives respect= > to nuclear displacements. Does any one know about a program capable of doing this= > > Thanks in advance. > > I immediately received a number of useful replies, that are > summarized below. Thank you to all that replied! > >&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&6666 > >>Date: Fri, 22 Nov 1996 12:04:28 -0800 >>From: jxh@msi.com (Joerg Hill) > >>As far as I know, CADPAC can do this. I've seen papers from Handy's group >>on third derivatives using CADPAC. >> >>Joerg-R. Hill >> >&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& &&&&&& >>From: buyong@ibmnla.chem.uga.edu >>Date: Fri, 22 Nov 1996 14:13:59 -0500 >> >>Program PSI developed in Professor Schaefer's group, center for >>computational chemistry, University of Geogia, Athens, GA 30602. >> The cost to do the analytical energy third derivative is very high. >>Presently, it is only applicable to small molecules at SCF level. >>see Buyong Ma, Yukio Yamaguchi, Henry F. Schaefer >> Molecular Physics, 1995, v86 N6, 1331 and references cited therein. >> >>================================================================= >>Buyong Ma buyong@ibmnla.chem.uga.edu >>Computational Center for Molecular Structure and Design >>Department of Chemistry >>University of Georgia >>Athens, Georgia 30602 USA Voice (706) 542-2044 >>================================================================= >> >&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&& > >>From: Ole Swang >>Date: Sun, 24 Nov 1996 12:32:45 +0100 (MET) >>To: xavier >>Subject: Re: CCL:3RD derivatives >> >> >> >>Dear Xavier, >> >>Trygve Helgaker's group is working on it - I'm not sure how far they have >>come. Try an Email to Kenneth Ruud (kenneth@kjemi.uio.no). >> >> Good luck, >> >> Ole Swang >> >> >&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&& > > /-------------------------------------------------------/ / Xavier Fradera i Llinas - IQC - Universitat de Girona / / E-mail: xavier@stark.udg.es / /-------------------------------------------------------/