From jsl@virgil.ruc.dk Thu Jun 19 04:49:58 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id EAA08315; Thu, 19 Jun 1997 04:08:40 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id KAA23688; Thu, 19 Jun 1997 10:14:09 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 19 Jun 97 10:07:19 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 19 Jun 97 10:07:10 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Kenneth Geisshirt Date: Thu, 19 Jun 1997 10:07:06 +0100 Subject: Re: CCL:semantics: molecular modelling CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <26EF0DF487C@virgil.ruc.dk> Kenneth: This is a never ending story! > Jens, your definition of computational chemistry is also too limited. I > regard the use of artificial intelligence in chemistry as computational > chemistry as well. A more appropriate definition could be: > > Computational chemistry is the application of any computational method > in chemistry. Computational method is understood to be any algorithm > implemented on a computer. I agree that artificial intelligence and probably stille more aspects should be considered, but I disagree with your definition in so far as it is limited to 'any algoritm implemented on a computer'. Computational chemistry started long before the invention of any mechanical or electronic computer; computations can be carried out with pencil and paper, or even in your mind! Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757781 + 2710 Roskilde University (RUC) Fax: +45 46757721 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://frederik.ruc.dk/dis/chem/psos =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Bernard.B.Pirard@GBJHA.zeneca.com Thu Jun 19 07:49:59 1997 Received: from bath.mail.pipex.net for Bernard.B.Pirard@GBJHA.zeneca.com by www.ccl.net (8.8.3/950822.1) id HAA09213; Thu, 19 Jun 1997 07:32:18 -0400 (EDT) X400-Received: by mta bath.mail.pipex.net in /PRMD=pipex/ADMD=pipex/C=gb/; Relayed; Thu, 19 Jun 1997 12:31:19 +0100 X400-Received: by /PRMD=ZENECA/ADMD=PIPEX/C=GB/; Relayed; Thu, 19 Jun 1997 12:26:01 +0100 Date: Thu, 19 Jun 1997 12:26:01 +0100 X400-Originator: Bernard.B.Pirard@GBJHA.zeneca.com X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=ZENECA/ADMD=TMAILUK/C=GB/;970619112601] 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--ua2XC2jGsGsvtYwMF5oRo9bVIdm8VTJW-- From DEVA@XRAY.BMC.UU.SE Thu Jun 19 12:50:09 1997 Received: from columba.udac.uu.se for DEVA@XRAY.BMC.UU.SE by www.ccl.net (8.8.3/950822.1) id MAA12854; Thu, 19 Jun 1997 12:21:45 -0400 (EDT) Received: from XRAY.BMC.UU.SE ([130.238.37.10]) by columba.its.uu.se with SMTP id <7504-38428>; Thu, 19 Jun 1997 18:21:23 +0100 Date: Thu, 19 Jun 1997 17:48:56 +0300 (MET-DST) From: DEVA@XRAY.BMC.UU.SE Message-Id: <970619174856.2020bf4f@XRAY.BMC.UU.SE> Subject: redox potential To: chemistry@www.ccl.net X-Vmsmail-To: SMTP%"chemistry@www.ccl.net" Hi All, I would like to know if the redox potential of an Fe-S cluster in a protein can be calculated. If so, what level of theory should give reasonable results in a reasonable time, and what programs should one use. Thanks in advance. I will summarize if there is any interest. Deva ------------------------------------------------------------------------- Devapriya Choudhury Deptt. of Molecular Biology Biomedical Center Uppsala,Sweden e-mail: deva@xray.bmc.uu.se ------------------------------------------------------------------------- From ccl@www.ccl.net Fri Jun 13 15:48:44 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA00608; Fri, 13 Jun 1997 15:28:52 -0400 (EDT) Received: from po6.andrew.cmu.edu for mm6n+@andrew.cmu.edu by bedrock.ccl.net (8.8.3/950822.1) id PAA00648; Fri, 13 Jun 1997 15:28:51 -0400 (EDT) Received: (from postman@localhost) by po6.andrew.cmu.edu (8.8.2/8.8.2) id PAA03978 for chemistry@ccl.net; Fri, 13 Jun 1997 15:28:51 -0400 Received: via switchmail; Fri, 13 Jun 1997 15:28:48 -0400 (EDT) Received: from unix12.andrew.cmu.edu via qmail ID ; Fri, 13 Jun 1997 15:26:46 -0400 (EDT) Received: from unix12.andrew.cmu.edu via qmail ID ; Fri, 13 Jun 1997 15:26:45 -0400 (EDT) Received: from mms.4.60.Jun.27.1996.03.02.53.sun4.51.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix12.andrew.cmu.edu.sun4m.54 via MS.5.6.unix12.andrew.cmu.edu.sun4_51; Fri, 13 Jun 1997 15:26:45 -0400 (EDT) Message-ID: Date: Fri, 13 Jun 1997 15:26:45 -0400 (EDT) From: Marcela Madrid To: chemistry@ccl.net Subject: CCL: PSC Sequence Analysis Workshop The Pittsburgh Supercomputing Center is offering a NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS workshop, July 20-25, 1997. This intense workshop will teach the basics of sequence analysis, including remote supercomputing, database searching and pairwise sequence alignment, multiple sequence alignments, pattern identification, inverse structure prediction, and visualization of macromolecular structures. Special emphasis will be placed on parameter selection, and the mathematical and statistical properties of the algorithms and methods presented. Information will also be presented on the latest pattern identification techniquesincluding hidden markov models, advanced position-specific weight matrix techniques and bayesan estimation. The workshop will consist of both lectures and extensive hands-on lab sessions. In addition to the lab exercises, participants can work on their own research problems, with the help of the instructors. Participants are encouraged to bring their research data, but not required. Instructors Dr. Gary Churchill, Cornell University Dr. David W. Deerfield II, Pittsburgh Supercomputing Center Dr. Michael Gribskov, San Diego Supercomputer Center Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center Alexander J. Ropelewski, Pittsburgh Supercomputing Center For more information, please see http://www.psc.edu/biomed/workshops/wk-97/NAPSA-97/napsa.html or contact Nancy Blankenstein, biomed@psc.edu, (412) 268-4960. To register, please send the following registration form to biomed@psc.edu Registration deadline is July 20, 1997. _____________________________________________________________________________ Pittsburgh Supercomputing Center Biomedical Supercomputing Initiative APPLICATION FORM Please complete the following form and return it with the corresponding documentation. Direct inquiries to: Nancy Blankenstein biomed@psc.edu or (412) 268-4960. Application Deadline: July 20, 1997 PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP, July 20-25, 1997. APPLICATION Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: ___________________________________________________ How did you learn about this workshop:_______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation >from a faculty member. Please return all application materials six weeks before the workshop you are applying for to Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein biomed@psc.edu, or (412)268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From black@cope.claremont.edu Thu Jun 19 13:50:05 1997 Received: from cope.claremont.edu for black@cope.claremont.edu by www.ccl.net (8.8.3/950822.1) id NAA13249; Thu, 19 Jun 1997 13:01:42 -0400 (EDT) Received: by cope.claremont.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA24453; Thu, 19 Jun 1997 09:49:15 -0700 From: "Kersey Black" Message-Id: <9706190949.ZM24451@cope.claremont.edu> Date: Thu, 19 Jun 1997 09:49:09 -0700 In-Reply-To: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) "SPARTAN: Summary: Symmetry Bug" (May 11, 4:56pm) References: <3204440@isis.Reed.EDU> X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman), chemistry@www.ccl.net, sparlist@wavefun.com, sparlist@nissan.wavefun.com, "Wayne Huang" Subject: Re: SPARTAN: Summary: Symmetry Bug Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On May 11, 4:56pm, Alan Shusterman wrote: > Subject: SPARTAN: Summary: Symmetry Bug > The following note summarizes replies and answers I received to my question > about an apparent symmetry bug in Spartan 4.1. > > Here is my original post: > -------------------------------- > I run into the following bug every few weeks: > > I build a molecule with a certain symmetry (Cs in this case) and optimize its > structure with symmetry ON. Then I try to reoptimize its structure with a > larger basis set while still using symmetry, but Spartan stops with the > following error message: > I have truncated the message and rely on memories for some of the details. It is ironic that this should cross my desk so recently because I confronted a similar symmetry problem this morning, however I just discoved while writing this that it is a feature, and not a bug. I share the problem with the list because others may want to know about this if planing to use the DFT methods. The bottom line is that symmetry when using DFT in 4.1.1 is not supported. Also, the use of constraints is not supported. Thus, I got caught in the following bind. I exploited the Cs symmetry of a transition state (C1 ground states) to effectively constrain it while "geometry optimizing" to a transition state stationary point with that symmetry. This approach worked well at the PM3(tm) level, but when I went to DFT the symmetry was turned off by Spartan and every thing proceeded as if C1. As a consequence the structure optimized towards a ground state structure. This leaves me trying to find a transition state on a relatively flat surface using the Transition State option and C1 symmetry. Wish me luck. I discover in the on-line help that nosymmetry is the default in DFT. I hope that this gets corrected in future versions. The inability to use symmetry this way makes calculations much more costly and more difficult, and makes the DFT options substantially less valuable. Cheers Kersey Black -- <::::::::::::::::::::::> Kersey Black Associate Professor of Chemistry Claremont McKenna, Pitzer, Scripps Colleges 925 N. Mills Ave Claremont, CA 91711-5916 black@cope.claremont.edu From ccl@www.ccl.net Tue Jun 17 18:49:36 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id RAA21761; Tue, 17 Jun 1997 17:57:29 -0400 (EDT) Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by bedrock.ccl.net (8.8.3/950822.1) id RAA26079; Tue, 17 Jun 1997 17:57:28 -0400 (EDT) Message-Id: <199706172157.RAA26079@bedrock.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 3375; Tue, 17 Jun 97 16:57:31 CST Date: Tue, 17 Jun 97 16:53:36 CST From: "Tapas Kar, Ph.D, Asst. Scientist" To: chemistry@ccl.net Subject: CCSD for excited states Hi, I am looking for programs to calculate excited state proton transfer process using Coupled-cluster method (EOM-CCSD/T). Please send mail directly to me I will summerize it. Tapas From gadre@chem.unipune.ernet.in Wed Jun 18 01:49:39 1997 Received: from sangam.ncst.ernet.in for gadre@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id BAA22629; Wed, 18 Jun 1997 01:12:21 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id KAA00355 for ; Wed, 18 Jun 1997 10:49:39 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA09760; Wed, 18 Jun 1997 10:39:33 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id KAA29210; Wed, 18 Jun 1997 10:38:49 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id KAA16053; Wed, 18 Jun 1997 10:53:39 -0500 Date: Wed, 18 Jun 1997 10:53:39 -0500 From: gadre@chem.unipune.ernet.in (Prof. Shridhar R. Gadre) Message-Id: <199706181553.KAA16053@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Deadline : ICCCRE XII Registration fee Dear Sirs : The Registaration fees for the XII ICCCRE (US$150 for bonafide students and $300 for others) may be paid before July 31, 1997. Please send a Banker's draft drawn on the State Bank of India (Pune DG branch) payable to The Registrar, University of Pune (ICCCRE). Thanks..............................Shridhar Gadre Convenor, XII ICCCRE From ccl@www.ccl.net Wed Jun 18 11:49:55 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA00301; Wed, 18 Jun 1997 10:50:59 -0400 (EDT) Received: from admiral.umsl.edu for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA17071; Wed, 18 Jun 1997 10:50:57 -0400 (EDT) Received: from chewwels.umsl.edu (chewwels.umsl.edu [134.124.105.177]) by admiral.umsl.edu (8.8.5/8.7.2) with SMTP id JAA27813 for ; Wed, 18 Jun 1997 09:50:56 -0500 (CDT) Message-Id: <3.0.1.32.19970618095342.00756f8c@jinx.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 18 Jun 1997 09:53:42 -0600 To: chemistry@ccl.net From: William Welsh Subject: AMBER 4.1 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Netters, I would like to know of possible sources of AMBER 4.1. Thanks ... Bill Welsh Dept. of Chemistry University of Missouri-St. Louis From jim.henshaw@aeat.co.uk Wed Jun 18 13:50:00 1997 Received: from aeat.co.uk for jim.henshaw@aeat.co.uk by www.ccl.net (8.8.3/950822.1) id MAA01568; Wed, 18 Jun 1997 12:51:10 -0400 (EDT) Received: from ccgate.aeat.co.uk by aeat.co.uk (8.8.5/AEAT-GW-1.6) id RAA10908; Wed, 18 Jun 1997 17:51:08 +0100 (BST) Received: from ccMail by ccgate.aeat.co.uk (IMA Internet Exchange 2.02 Enterprise) id 3A80FD60; Wed, 18 Jun 97 17:41:58 +0100 Mime-Version: 1.0 Date: Wed, 18 Jun 1997 17:21:38 +0100 Message-ID: <3A80FD60.1268@ccgate.aeat.co.uk> From: jim.henshaw@aeat.co.uk (Jim Henshaw) Subject: MOPAC Thermo Calc's on PC's To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Hi, I am a relatively new user of MOPAC, which I have been using on a number of Pentium PC's (different operating systems, Windows 3.1, 95 etc.). I am trying to calculate thermodynamic properties of several planar polyaromatic compounds, 10 to 30 C atoms, 10 to 30 H atoms. In some of these systems a H, CH3 or CH3CH2 radical sits above the aromatic plane (above a C atom), distorting the plane, as aromatic carbon atoms change from sp2 to sp3 hybridisation. I have several questions which MOPAC users may or may not be able to help me with. 1. Has any one carried out calculations on molecular systems similar to those I have described ? 2. Does any one have any general hints in using the THERMO key word, for example it seems to work better if I include the XYZ keyword and I have optimised the geometry using PRECISE. 3. For some of the molecules I am looking at, MOPAC version 7.0 performs the thermodynamic calculation OK, while version 6.0 does not? What is the reason for this? I have not investigated this fully yet using debugging keywords, but I intend too. 4. Does anyone have any general hints/comments in relation to using MOPAC on a PC ? 5. Does any one know of a MOPAC version 7.0 that runs under Windows 95 ? Thanks to anybody who replies to any of my questions, and I will of course summarise any answers I obtain for general consumption. Regards Jim From ccl@www.ccl.net Wed Jun 18 19:55:36 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id TAA06105; Wed, 18 Jun 1997 19:43:19 -0400 (EDT) Received: from ariz.library.ucsb.edu for huber@library.ucsb.edu by bedrock.ccl.net (8.8.3/950822.1) id TAA05061; Wed, 18 Jun 1997 19:43:09 -0400 (EDT) Received: by ariz.library.ucsb.edu (5.65/DEC-Ultrix/4.3) id AA08673; Wed, 18 Jun 1997 16:42:52 -0700 Date: Wed, 18 Jun 1997 16:42:51 -0700 (PDT) From: Chuck Huber To: chemed-l@uwf.cc.uwf.edu, chemind-l@derwent.co.uk, chemistry@ccl.net, chminf-l@listserv.indiana.edu, piug-l@derwent.tecc.co.uk Subject: FINAL CALL -- 1998 Herman Skolnik Award Nominations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The following message has been posted to the Chemical Information, Patent Information Users Group, Chemical Education, Chemical Structure Indexing and Computational Chemistry listservs. Please excuse any duplication. Please note that the deadline is JULY 1, 1997. Chuck Huber Davidson Library University of California Santa Barbara huber@library.ucsb.edu Call for Nominations The American Chemical Society Division of Chemical Information (CINF) --------------------------------------------------------------------------- 1998 Herman Skolnik Award --------------------------------------------------------------------------- The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honor of the first recipient, Herman Skolnik. By this Award, the Division of Chemical Information hopes to encourage the continuing advancement of chemical information science in areas such as: Design of new and unique computerized information systems; Preparation and dissemination of chemical information; Editorial innovations; Design of new indexing, classification, and notation systems; Chemical nomenclature; Structure-activity relationships; and Numerical data correlation and evaluation. The Award consists of a $2000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. The 1998 Award Symposium will take place at the 216th American Chemical Society National Meeting in Boston on Tuesday, August 25, 1998. In recent years, the Award Symposium has been organized by the recipient. Since its establishment in 1976, the Award has been presented to the following individuals at a national ACS meeting: Herman Skolnik 1976 Eugene Garfield 1977 Fred A. Tate 1978 William J. Wiswesser 1980 Ben H. Weil 1981 Robert Fugmann 1982 Russell J. Rowlett, Jr. 1983 Montagu Hyams 1984 Dale B. Baker 1986 William Theilheimer 1987 David R. Lide, Jr. 1988 Michael F. Lynch & Stuart A. Marson 1989 Ernst Meyer 1990 W. Todd Wipke 1991 Jacques-Emile Dubois 1992 Peter Willett 1993 Alexandru T. Balaban 1994 Reiner Luckenbach & Clemens Jochum 1995 Milan Randic 1996 Johann Gasteiger 1997 Nomination letters should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. The deadline for nominations for the 1998 Award is July 1, 1997. Nominations should be sent to: Charles F. Huber CINF Awards Chair Davidson Library University of California Santa Barbara, CA 93106 Phone: (805)893-2762 Fax: (805)893-8620 E-mail: huber@library.ucsb.edu From bausch@chem.vill.edu Thu Jun 19 14:50:04 1997 Received: from rs6chem.chem.vill.edu for bausch@chem.vill.edu by www.ccl.net (8.8.3/950822.1) id NAA14262; Thu, 19 Jun 1997 13:57:13 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with SMTP id OAA16977 for ; Thu, 19 Jun 1997 14:02:31 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jun 1997 01:58:50 -0500 To: chemistry@www.ccl.net From: bausch@chem.vill.edu (Joseph W. Bausch) Subject: symmetry of transition states I hope this question is meaningful and understandable. I am curious about the symmetry of a transition state connecting molecule A to an isomeric structure B. Are there any "rules" governing the symmetry of the transition state as it relates to the symmetry of A and B? For instance, say both A and B have C1 symmetry. Must the transition state have C1 symmetry, or can it have some higher symmetry group like Cs? I'll summarize if there is sufficient interest. JWB -------- From buyong@ibmnla.chem.uga.edu Thu Jun 19 14:57:55 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id NAA14222; Thu, 19 Jun 1997 13:55:34 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id NAA18954; Thu, 19 Jun 1997 13:55:32 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA14784; Thu, 19 Jun 1997 13:55:12 -0400 Date: Thu, 19 Jun 1997 13:55:10 -0400 (EDT) To: Dr Lutz Ackermann Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:semantics : molecular modelling In-Reply-To: <199706181456.PAA25505@faraday.ri.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Ackermann: I read your comments with a great interest. Your views and diagram have much overlap with my understanding about the philosophy of computational chemistry, which may be seen in web site: http://alphanla.chem.uga.edu/~buyong/philo/philo.html My philosophy of computational chemistry is that it is like analytical chemistry. However, our instruments are computers, and no real substance is involved in our observation. For analytical chemistry, one may have powerful instruments, such as high resolution NMR, IR, etc; one may also use simple wet analysis. For computational chemistry, we have a lot of ways too, such as quantum mechanical methods, molecular mechanics, molecular dynamics, QSAR.... In a broad definition, you may write an equation: computational chemistry = molecular modeling, just like the general guidelines of "The Journal of Molecular Modeling". QUESTION: HOW TO DEFINE "ANALYTICAL CHEMISTRY"?? ================================================================= Dr. 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 ================================================================= On Wed, 18 Jun 1997, Dr Lutz Ackermann wrote: > Jeffrey L. Nauss wrote: > > > Molecular modelling would be the application of some form of a model to > > studying molecular structure. > > I agree with Jeffrey that although the term MM is normally used to > indicate a certain type of method (i.e. empirical methods etc). > one could well use it in a wider sense, comprising almost anything > that has to do with the theory of molecules. If one follows this > thought a bit further, it seems, however, that "MM" becomes a > doubling of terms and that expressions like > > > Watson and Crick constructed a model of a molecule ... > > are tautological, because "molecule" itself, in the framework of the theory > of matter, is a model (so what's a 'model of model'?) > Jeffrey also mentions > > hand-held CPK models and simple drawings on paper > For the reason just given it would then be semanically corret > to say "this molecule ..." while pointing at a picture > on a computer screen (well, one could introduce another category, > the "representation" of a model/molecule to refere to the actual drawing, > input file etc). > > Of course 'model of a molecule' could refere to > 'a simplified version of a molecular model', where the simplification > could either be of chemical nature (e.g. replace CH3 by H group) or > could point to the principal fact that different models describe > physical reality with a variing degree of crudeness (or approximation) > and no model covers all aspects of a theory. > For example: if A' is a molecular model that includes vibrational aspects, > and A" is a rigid version of A', one could say, that > > (1) A" is a model of the molecule A'. > ----- -------- > I do, however prefere to say: > > (2) both A' and A" are (different) models of the same physical reality > ------ > > But what, then, is THE MOLECULE? Well take all the models A', A", A''' etc. > i.e. all that is known about a compound and call it A. So A would be a > model that includes every known fact about a given substance. Therefore > A is the molecule. > > Maybe these semantic differences could be depicted in a little plot: > > > physical reality > > | | | > --------------------- | -------------------- | ------- | ------- > > V V V > > Theory A' A' A" > > | or > V > > A" > --------------------------------------------------------------------- > > representation: a drawing, a set of coordinates ... > > > (1) (2) > > > > Very well so far, but where does A go? > I think the semantic problem arises, because some people (mostly subconcsiously) > introduce another 'layer' between theory and reality to accomodate A, THE MOLECULE. > Some would even forget about the fact, that molecules are models of reality and > place A in the upper section of the diagram above. The reason for this probably > being, that "molecule" is a very succesfull and extremely usefull concept to > which we have got used very much. > > Ok, that's been it, folks. I am afraid, I didn't have much time to explain these > philosophical aspects in to much detail, but you shold be able to get the gist > of what I am trying to say. Comments? > > > <^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^> > < Dr. Lutz Ackermann > > < Research Assistent > > < The Royal Institution of Great Britain > > < Davy-Faraday Research Laboratory > > < 21 Albemarle Street > > < London W1X 4BS > > < UK > > < > > < phone: +44-171-409 2992 ext 424 > > < FAX: +44-171-629 3569 > > < e-mail: lutz@ri.ac.uk > > < http://www.ri.ac.uk/DFRL/L.Ackermann > > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: lutz@ri.ac.uk > -- Original Sender From: Address: lutz@ri.ac.uk > 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 sichelj@UMoncton.ca Thu Jun 19 15:50:07 1997 Received: from bosoleil.ci.umoncton.ca for sichelj@UMoncton.ca by www.ccl.net (8.8.3/950822.1) id PAA16393; Thu, 19 Jun 1997 15:41:53 -0400 (EDT) Received: by bosoleil.ci.umoncton.ca (1.37.109.20/16.2) id AA217489403; Thu, 19 Jun 1997 16:43:24 -0300 Date: Thu, 19 Jun 1997 16:43:23 -0300 (ADT) From: "J. Sichel" Subject: Re: CCL:symmetry of transition states To: "Joseph W. Bausch" Cc: chemistry@www.ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 19 Jun 1997, Joseph W. Bausch wrote: > I hope this question is meaningful and understandable. I am curious about > the symmetry of a transition state connecting molecule A to an isomeric > structure B. Are there any "rules" governing the symmetry of the > transition state as it relates to the symmetry of A and B? Yes there are rules. Try the book by R.G.Pearson "Symmetry rules for chemical reactions" (Wiley 1976). > For instance, say both A and B have C1 symmetry. Must the transition state > have C1 symmetry, or can it have some higher symmetry group like Cs? The transition state can have higher symmetry than either reactant or product. A simple example is the inversion of ammonia: reactant and product are C3v and the planar transition state is D3h. If you consider instead inversion of NHFCl, then reactant and product are C1 and the planar transition state is Cs as you have asked. John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada From buyong@ibmnla.chem.uga.edu Thu Jun 19 16:50:06 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id QAA16794; Thu, 19 Jun 1997 16:08:24 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id QAA24218; Thu, 19 Jun 1997 16:08:26 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA18818; Thu, 19 Jun 1997 16:08:08 -0400 Date: Thu, 19 Jun 1997 16:08:05 -0400 (EDT) To: "Joseph W. Bausch" Cc: chemistry@www.ccl.net Subject: Re: CCL:symmetry of transition states In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII you may contact Professor Schaad, L. J in VANDERBILT UNIV,DEPT CHEM,BOX 1583/NASHVILLE//T/37235. He has given several talks on the symmetry rules for transition state. However, it seems that there is no formal publication yet. ================================================================= Dr. 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 ================================================================= On Thu, 19 Jun 1997, Joseph W. Bausch wrote: > I hope this question is meaningful and understandable. I am curious about > the symmetry of a transition state connecting molecule A to an isomeric > structure B. Are there any "rules" governing the symmetry of the > transition state as it relates to the symmetry of A and B? > > For instance, say both A and B have C1 symmetry. Must the transition state > have C1 symmetry, or can it have some higher symmetry group like Cs? > > I'll summarize if there is sufficient interest. > > JWB > -------- > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bausch@chem.vill.edu > -- Original Sender From: Address: bausch@chem.vill.edu > 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 pyadav@njmsa.UMDNJ.EDU Thu Jun 19 17:34:54 1997 Received: from njmsa.UMDNJ.EDU for pyadav@njmsa.UMDNJ.EDU by www.ccl.net (8.8.3/950822.1) id RAA17318; Thu, 19 Jun 1997 17:02:29 -0400 (EDT) Received: (from pyadav@localhost) by njmsa.UMDNJ.EDU (8.7.6/8.7.3) id RAA29930 for chemistry@www.ccl.net; Thu, 19 Jun 1997 17:02:30 -0400 (EDT) From: Prem Yadav Message-Id: <199706192102.RAA29930@njmsa.UMDNJ.EDU> Subject: mol. modeling & comp. Chemistry To: chemistry@www.ccl.net Date: Thu, 19 Jun 1997 17:02:30 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit What I feel about molecular modeling: Molecular modeling is a complete protocol to establish a relationship between molecular structure and its function. Function may be chemical or biological. The final result is called a "Model". To arrive at final stage, the requirement is the knowledge of structure, chemical properties and biological and/or chemical function. Computational chemistry is a tool which contribute in finding the structure and chemical properties of the molecular system. Structure may come >from any experimental tool also. ------------------------------------------------------------------------ Prem Yadav, Ph.D. IST-Academic Computing Center University of Medicine & Dentistry of NJ Voice: 908-235-4172 Room No. SB-11 Fax: 908-235-5252 675 Hoes Lane Email: pyadav@umdnj.edu Piscataway, NJ 08854-5635 http://www.umdnj.edu/~pyadav/prem.html ------------------------------------------------------------------------- From ans@crystal.uwa.edu.au Thu Jun 19 23:50:06 1997 Received: from acheron.uwa.edu.au for ans@crystal.uwa.edu.au by www.ccl.net (8.8.3/950822.1) id XAA19048; Thu, 19 Jun 1997 23:45:05 -0400 (EDT) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by acheron.uwa.edu.au (8.8.2/8.8.0) with SMTP id LAA18826 for ; Fri, 20 Jun 1997 11:44:53 +0800 (WST) Received: from hewl.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA10139; Fri, 20 Jun 1997 14:41:16 +0800 From: ans@crystal.uwa.edu.au (Alexandre N. Sobolev) Message-Id: <9706200411.AA03934@hewl.crystal.uwa.edu.au> Subject: Paking in the unit cell To: chemistry@www.ccl.net Date: Fri, 20 Jun 97 12:11:58 WST Mailer: Elm [revision: 70.85] > > Hi > Along these same lines, I am seeking a program that will allow one to > build a lattice of molecules by inputting one or several different > molecular files as well as the unit cell dimensions. I currently have a > routine called bcell that will make a lattice of multiple copies of the > SAME molecule file, but I need a routine that will allow a lattice to be > built which will contain multiple copies of one molecule in the lattice, > as well as ONE that is different. > > Anyone have any suggestions? > > Richard > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: woods@draco.pmmp.uic.edu > -- Original Sender From: Address: woods@draco.pmmp.uic.edu > 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 > > Dear Richard, Everyone hwo uses Siemens' SHELXTL software for X-ray molecular structure determination can do it. Contact to Susan Byram (e-mail: sbyram@siemens-xray.com) at Siemens Analitical in Madison, Wisconsin, USA or Eric Hovestreydt (e-mail: hovestr@khe.scn.de) at AXS in Karlsruhe, Germany Regards Alexandre N. Sobolev Department of Chemistry The University of Western Australia Nedlands, Perth 6907, W.A. Australia e-mail: ans@crystal.uwa.edu.au