From heelisp@delta.newi.ac.uk Mon Apr 24 08:19:09 1995 Received: from delta for heelisp@delta.newi.ac.uk by www.ccl.net (8.6.10/930601.1506) id IAA06311; Mon, 24 Apr 1995 08:11:58 -0400 From: Date: Mon, 24 Apr 1995 13:06:01 +0100 Message-Id: <95042413060145@delta.newi.ac.uk> To: chemistry@ccl.net Subject: CCL summary, residue exposure to solvent" X-VMS-To: SMTP%"chemistry@ccl.net" From Paul Heelis North East Wales Institute UK Recently I posted the following request for help on analyzing solvent exposure of residues in proteins. Thanks to all who replied. Here's a summary of the replies The original posting > Does anyone know of a program that can analyse a Brookhaven PDB file and determine the degree of exposure of a particular residue to the surrounding solvent and/or measure the effective dielectric constant of its environment. *********************************************************** From: SMTP%"polowin@hyper.hyper.com" To: heelisp CC: Subj: Re: CCL:PDB files, residue solvent exposure Hi, Paul. The first part can be done with HyperChem and the QSAR Properties module of ChemPlus. One would select each residue, one at a time, and import the complete structure into the module. The solvent-accessible area is calculated only for the selected part. The process would be automated by an Excel macro or a Visual Basic program. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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 *********************************************************** From: SMTP%"tripos!rigel!david@uunet.uu.net" To: heelisp CC: Subj: Re: CCL:PDB files, residue solvent exposure Paul, The upcoming 6.2 release of Sybyl from Tripos includes a new module called ProTable for the analysis of protein structures. In addition to numerous other quantities, ProTable displays the relative solvent accessibility of each residue in a protein structure. It uses the latest version of SAVOL from Bob Pearlman and colleagues at the University of Texas, Austin to compute the solvent accessibile surface areas for each atom. Let me know if you'd like more information. David Mosenkis (david@tripos.com)Tripos, Inc. *********************************************************** From: SMTP%"goulpj@essex.ac.uk" To: heelisp CC: Subj: Re: CCL:PDB files, residue solvent exposure Hi Paul, There is a program called whatif around. we use it alot here.It is free to Academia you can get it from Gert Vriend at EMBL It is an alround great program that does lots and lots of different things. I can not remember his email but i reckon you should be able to find him pretty easily . *********************************************************** From: SMTP%"V050PFB6@ubvms.cc.buffalo.edu" To: heelisp@delta.newi.ac.uk CC: Subj: Re: PDB files, residue solvent exposure Hi Paul, The authors are Habsch and Sander. the ref. is Biopolymers vol 22 (1983) pp 2577-2637. The paper says DSSP will be avail. from PDB, but I think we wrote directly to Sander. Sander's e-mail address is Chris.Sander@EMBL-Heidelberg.DE see ya, Don *********************************************************** From: SMTP%"tripos!carme!akbar@uunet.uu.net" To: uunet!delta.newi.ac.uk!heelisp@uunet.uu.net CC: Subj: Re: CCL:PDB files, residue solvent exposure Dear Paul, A Sybyl module called ProTable is to be released this summer with version6.2 of Sybyl. ProTable, besides having the functionality of calculatingresidue solvent exposures, also provides a number of different descriptorsfor the residues in a protein. The solvent accessibility calculation isbased on SAVOL, a program from Prof. Robert Pearlman and collegues atTexas, Austin. It is very efficient and accurate. Sincerely, Akbar NayeemBiopolymer Scientist, Tripos Inc. ***********************************************************Subj: Re: CCL:PDB files, residue solvent exposure Hi again, His e-mail address is Gert.Vreind@EMBL-Heidelberg.de He is not around for a while but you can still give him a try. He is in Brazil or some such place. Paul ================== RFC 822 Headers ================== *********************************************************** From: SMTP%"arne@hodgkin.mbi.ucla.edu" To: heelisp@delta.newi.ac.uk CC: Subj: CCL:PDB files, residue solvent exposure I guess you have received somethng usefull by now. All (?) the major Molecular mechanics packages does this. I use the algorithm by Legrand & Merz (JCC 1993) and could probably makeyou a quick hack if you do not find anything else. (at the moment the routines are incorporated in a way too big program). Unfortunatelyit is in fortran, so you'd need a fortran compiler. arne *********************************************************** From: SMTP%"Antoine.Daruvar@embl-heidelberg.de" To: heelisp CC: Subj: Re: DSSP Dear Paul Heelis, DSSP is sent via e-mail as a C source code that can be compile on any system (having a C compiler). Information for the compilation are sent together with the program. Antoine de Daruvar From eslone@osf1.gmu.edu Mon Apr 24 08:47:55 1995 Received: from osf1.gmu.edu for eslone@osf1.gmu.edu by www.ccl.net (8.6.10/930601.1506) id IAA06677; Mon, 24 Apr 1995 08:42:12 -0400 Received: by osf1.gmu.edu; (5.65v3.0/1.1.8.2/07Sep94-1001AM/GMUv1) id AA17077; Mon, 24 Apr 1995 08:42:11 -0400 Message-Id: <9504241242.AA17077@osf1.gmu.edu> Subject: Clarification on trivia question To: chemistry@ccl.net Date: Mon, 24 Apr 1995 08:42:10 -0400 (EDT) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL24alpha5] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1322 I've had alot of "please summarize" responses... but no submissions yet! One clarification though, I mean by my question 'what molecule is composed of the greatest number of different elements', so something like acetic acid would count as 3 (C, H, O). The molecule should also exist, naturally or synthetically, theoretical molecules don't count. I've seen a similar question for linguists (what English word uses the most different letters from the alphabet); and it would seem by the responses I've gotten so far, many people are curious like I am. I'd do a database search myself, but then how does one phrase this question to a database? It's not your typical query! Eric ________________________________________________________________________________ J. Eric Slone George Mason University Department of Chemistry Fairfax, Virginia 22030-4444 Internet: eslone@gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Pager: (202) 597-2373 Miguel de Unamuno Voice: (703) 461-7078 ________________________________________________________________________________ From ernst@bkfug.kfunigraz.ac.at Mon Apr 24 09:47:56 1995 Received: from balu.kfunigraz.ac.at for ernst@bkfug.kfunigraz.ac.at by www.ccl.net (8.6.10/930601.1506) id JAA07506; Mon, 24 Apr 1995 09:39:14 -0400 Received: from bkfug.kfunigraz.ac.at by balu.kfunigraz.ac.at with SMTP (1.37.109.16/16.2) id AA267090335; Mon, 24 Apr 1995 15:32:15 +0200 Received: by bkfug.kfunigraz.ac.at (MX V4.1 AXP) id 99; Mon, 24 Apr 1995 15:37:51 +0100 Date: Mon, 24 Apr 1995 15:37:50 +0100 From: margot To: eslone@osf1.gmu.edu Cc: chemistry@ccl.net Message-Id: <0098F5E1.D29ABF26.99@bkfug.kfunigraz.ac.at> Subject: RE: CCL:Clarification on trivia question :I've had alot of "please summarize" responses... but no submissions yet! :One clarification though, I mean by my question 'what molecule is :composed of the greatest number of different elements', so something :like acetic acid would count as 3 (C, H, O). The molecule should also :exist, naturally or synthetically, theoretical molecules don't count. According to "The Name Game" by A. Nickon and E. F. Silversmith, Pergamon 1987, p. 149 a compound containing 10 elements: C60H78Br2CdCl2I2N16O2P2W2 I'm not going to quote the full name - I'd be typing for the next say 5 Minutes. I hope you can locate the reference! Someone at CAS dug it up originally, maybe it's outdated already. Have fun, margot Inst. f. Th. Chemie, Graz, Austria From desmond@om3.ch.umist.ac.uk Mon Apr 24 11:17:57 1995 Received: from nessie.mcc.ac.uk for desmond@om3.ch.umist.ac.uk by www.ccl.net (8.6.10/930601.1506) id LAA09770; Mon, 24 Apr 1995 11:04:27 -0400 Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 24 Apr 1995 16:03:29 +0100 Received: by om3.ch.umist.ac.uk (940406.SGI/) for chemistry%ccl.net@nessie.mcc.ac.uk id AA15734; Mon, 24 Apr 95 16:17:13 +0100 Date: Mon, 24 Apr 1995 16:17:13 +0100 (BST) From: Simon Collins Subject: Charges/bond-breaking To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am presently interseted in the varience of charge with energy for the heterolytic dissociation of various simple acids, such as HF. I am trying to do this by simply doing single point energies at varying increasing bond lengths, but the molecule splits up homolytically into the radicals. Is there any way round this problem? Any help would be gratefully received. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Simon Collins - Dept. Chemistry, UMIST, Manchester. M60 1QD Tel: 061-236-3311 x4476 Fax: 061-236-7677 E-mail: desmond@trigger.ch.umist.ac.uk S.Collins@umist.ac.uk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From bhardy@convex.ox.ac.uk Mon Apr 24 11:33:19 1995 Received: from oxmail2.ox.ac.uk for bhardy@convex.ox.ac.uk by www.ccl.net (8.6.10/930601.1506) id LAA09897; Mon, 24 Apr 1995 11:12:09 -0400 Received: from convex.ox.ac.uk by oxmail2.ox.ac.uk. with SMTP (PP) id <28986-0@oxmail2.ox.ac.uk.>; Mon, 24 Apr 1995 16:12:20 +0100 Received: (from bhardy@localhost) by convex.ox.ac.uk (1.1/8.6.12) id QAA23516 for CHEMISTRY@ccl.net; Mon, 24 Apr 1995 16:10:59 +0100 Date: Mon, 24 Apr 1995 16:10:59 +0100 From: Barry Hardy Message-Id: <199504241510.QAA23516@convex.ox.ac.uk> To: CHEMISTRY@ccl.net Subject: First Electronic Glycoscience Conference ELECTRONIC GLYCOSCIENCE CONFERENCE-1 ************************************ The First Electronic Glycoscience Conference (EGC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Sept 18 - Oct 13, 1995. This international conference will cover a broad range of disciplines related to carbohydrate and glycoconjugate molecules including chemical, physical, biological and medical areas using theoretical, experimental and computational approaches. EGC-1 will be a fully international event open to all members of our scientific community. It is our intent that EGC-1 will be an historic occasion from which we will move forward towards further annual conferences and virtual resource creation for The Glycosciences. Although the conference runs for what looks like a long period of time by traditional standards, it is anticipated that participants might often interweave the conference with other activities in their regular schedule and thus have the flexibility to come and go to the conference (flexi-conferencing). Participants should realise that this event is experimental and they should we willing to attend with a spirit of exploration and adventure. We believe that many glycoscientists will benefit from an exposure to methods that will revolutionize how we do science research and how we communicate as scientists. Also, in addition to the presentation of technical scientific information and results, we will use specific measures to strongly encourage cross-disciplinary communication in language intelligible to general scientists. For example, all technical papers will require an accompanying communication explaining the primary methods, results and conclusions of the paper in language accessible to a general scientific audience. During and after the conference we anticipate the formation of connections and cross-references between diverse areas of science and technology in the Glycosciences. Conference subject areas will include Glycosyltransferases, Glycoimmunology, Primary Structure Determination, Glycolipids, Organic Synthesis, Molecular Modeling, Design and Informatics, Lectins, Polysaccharides and Cellulose, Proteoglycans and Glycosaminoglycans, Therapeutics, Carbohydrate Biotechnology, Glycobiology, Crystallography, NMR, Function of Carbohydrates in Biological Systems, and Perspectives. Papers will be prepared in Hypertext Markup Language (HTML) and participants will view the papers via the World Wide Web. Aid and consultation will be provided to participants during summer '95 to help newcomers to the Web in the presentation of their conference paper. During the conference discussions will take place via email using a Net-based electronic mailing list. It is intended that papers will be refereed prior to publication in both traditional and electronic formats. In addition to a full technical paper authors will be required to produce a shortened version of their paper that will summarize the main approaches, results and conclusions of their work in language accessible to all general scientists. During EGC-1 participants will be able to register at a Virtual Conference Center (VCC) created by Gustavo Glusman and the administrators of BioMOO, a virtual meeting place for biologists, through Net-based telnet sessions into a Networked Virtual Environment. There they will be able to use their own rooms, schedule and attend meetings, hold private talks, take and exchange notes, visit interactive poster sessions, trade exhibits and an employment center, and socialize. During the conference participants will be able to contribute to a collective creative project: The Glycoscience Hyperglossary (GH). The GH will serve to define scientific terms and definitions of relevance to the Glycosciences through the collective contribution of entries and explanations to an electronic dictionary. The GH will be then be published with the conference papers as an international information resource subject to further refinement and evolution. ********* :-) ********** DEADLINES AND DATES 1) DO NOW - GIG mailing list Conference-related news and announcements will be posted regularly to the GIG mailing list and the bionet glycosci newsgroup. If you are not on the GIG list and want to be added to receive news on EGC-1 please email bhardy@convex.ox.ac.uk 2) DO NOW - Pre-Registration If you intend to participate in EGC-1 please email your name, institution, address, phone, fax, and email address using the template for registration enclosed at the end of this announcement. It should be emailed to wilson@edv1.boku.ac.at You should pre-register even if you are not presenting a paper. The deadline for pre-registration is Sept 1 1995. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of paper and poster abstracts is July 1st. Email your abstract directly to the appropriate section convener listed below. Your abstract should be no longer than 300 words. 4) DEADLINE for receipt of PAPER. The deadline for receipt of papers and posters is Sept 1st. You can either 1) deposit your text and graphics files at the conference ftp site or 2) send in the Web address from which you will serve the paper. 5) Conference Commencement The Conference will commence on Monday Sept 18th. The first week will be used by registrants to register, to familiarize themselves with their virtual surroundings and tools, and to commence reading of conference papers. 6) The Conference The main period of the conference will run from Monday Sept 25th to Friday October 13th during which discussions and meetings will take place. 7) Refereeing Period The refereeing period will commence upon completion of the conference. If you present a paper at EGC-1 you will be expected to contribute a refereeing evaluation on another conference paper. Referee reports will be due Friday November 10th. Final revised papers are due by Friday December 1st. Posters will not go through the refereeing process. ********* :-) ********** World Wide Web ************** Pages will be loaded on World Wide Web during Spring and Summer '95 that will provide further details on EGC-1 including guidance and advice in preparing paper text and graphics for display on the Web. ********* :-) ********** Poster Sessions *************** Poster sessions will consist of informal papers presented as Web pages which will be accompanied by discussions in the Virtual Conference Center. ********* :-) ********** Trade Center ************ The Conference will feature a Virtual Trade Center where commercial vendors, consultants, manufacturers, and contractors will be able to display their goods and services in return for donations of support to conference activities. ********* :-) ********** Job Center ********** The Conference will provide Job Services in the Virtual Job Center which will feature employment ads, interviews and aid in an interactive environment. ********* :-) ********** SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and paper) 1. Glycosyltransferases Harry Schachter, Hospital for Sick Children, Toronto, Canada Email: harry@resunix.ri.sickkids.on.ca 2. Glycoimmunology Roy Jefferis, University of Birmingham, UK Email: R.Jefferis@bham.ac.uk 3. Primary Structure Determination Dave Ashford, University of York, UK Email: da5@unix.york.ac.uk 4. Glycolipids Ronald L. Schnaar, Johns Hopkins University, Baltimore, USA Email: rschnaar@welchlink.welch.jhu.edu 5. Synthesis and Physical Organic Chemistry Tim Gallagher, University of Bristol, UK Email: T.Gallagher@bristol.ac.uk 6. Molecular Modeling, Design and Informatics Jerry Thomas, Rijksuniversiteit Utrecht, The Netherlands Email: jerry@RUUCJ5.chem.ruu.nl 7. Lectins Eric Toone, Duke University, USA Email: toone@chem.duke.edu 8. Polysaccharides and Cellulose Andrepeter Heiner, State Research Center, Finland Email: Andrepeter.Heiner@vtt.fi 9. Proteoglycans and Glycosaminoglycans Bob Lauder, University of Lancaster, UK Email: r.lauder@lancaster.ac.uk 10. Glycotherapeutics G Turner University of Newcastle, UK Email: G.A.Turner@newcastle.ac.uk 11. Carbohydrate Biotechnology Liz Hounsell, University College London Email: ehounsel@bsm.biochemistry.ucl.ac.uk 12. General Glycobiology Gerald W. Hart, University of Alabama at Birmingham, USA Email: gwhart@bmg.bhs.uab.edu 13. Crystallography Bill Winter, State University of New York, Syracuse, USA Email: wtwinter@mailbox.syr.edu 14. Nuclear Magnetic Resonance Steve Homans, University of St. Andrews, UK Email: swh@st-andrews.ac.uk 15. Function of Carbohydrates in Biological Systems Diana Blythe National Institutes of Health, USA Email: BlitheD@cc1.nichd.nih.gov 16. Glycoscience Perspectives: Past, Present and Future Barry J. Hardy, Oxford University, UK Email: bhardy@convex.ox.ac.uk Iain Wilson, Institut fuer Bodenkultur, Wien, Austria Email: wilson@edv1.boku.ac.at VIRTUAL CONFERENCE CENTER Manager John Towell, Northern Illinios University, USA Email: m50jft1@hayek.cob.niu.edu Aide Leonore A. Findsen, University of Hawaii, Hawaii, USA Email: leonore@uhunix.uhcc.hawaii.edu TECHNICAL CONSULTANT Alan Robinson Oxford University, UK Email: alan@physchem.chem.ox.ac.uk Alan Robinson is providing conference participants technical support now and during the conference. He will try and help you with questions related to using the Net/Web (setting up a server, writing hypertext), will be providing the group answers to frequently asked questions, and will provide advisory support on preparing papers on Web pages. When sending him a query please try to solve the problem first yourself. If you have a question please keep it clear and concise and place 'EGC QUERY' in your subject heading. CONFERENCE ORGANIZERS (Please email us with any general questions or comments) Barry J. Hardy Physical and Theoretical Chemistry Lab Oxford University, Oxford, OX1 3QZ, U.K. Email: bhardy@convex.ox.ac.uk Iain Wilson Institut fuer Chemie Universitaet fuer Bodenkultur Gregor-Mendel-Strasse 33 A-1180, Wien, Austria Email: wilson@edv1.boku.ac.at "The difficulty in imagining the future comes from the fact that the important changes are not quantitative. The important changes are qualitative, not bigger and better rockets but new styles of architecture, new rules by which the game of exploration is played." Freeman Dyson *** EGC-1 : The Glycosciences Breaking through Boundaries *********** ****** with New Styles of Architecture and Exploration ************** ******************************************************************** TEMPLATE FOR PRE-REGISTRATION: Please return the following card via email to wilson@edv1.boku.ac.at ------------EGC-1 REGISTRATION--------------------- NAME: INSTITUTION: ADDRESS: ADDRESS: PHONE: FAX: EMAIL: From chiremv!andromeda!martine@uunet.uu.net Mon Apr 24 12:47:57 1995 Received: from relay3.UU.NET for chiremv!andromeda!martine@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id MAA12505; Mon, 24 Apr 1995 12:47:45 -0400 Received: from uucp3.UU.NET by relay3.UU.NET with SMTP id QQymwh13919; Mon, 24 Apr 1995 12:47:41 -0400 Received: from chiremv.UUCP by uucp3.UU.NET with UUCP/RMAIL ; Mon, 24 Apr 1995 12:47:41 -0400 Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA09815; Mon, 24 Apr 95 09:59:37 PDT Received: by andromeda (931110.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry id AA24531; Mon, 24 Apr 95 09:37:58 -0700 Date: Mon, 24 Apr 95 09:37:58 -0700 From: chiremv!andromeda!martine@uunet.uu.net (Eric Martin) Message-Id: <9504241637.AA24531@andromeda> To: uunet!ccl.net!chemistry@uunet.uu.net Subject: CCL:Clarification on trivia question Hi Eric, I don't know the answer to the molecule composed of the greatest number of different elements, but I can suggest how to pose a query. If you have access to the Daylight database software with the Sprezzi (sp?) database, a sort by the length of the molecular formula should get you close. Then, taking the top cut from there, find the molecular formula with the most capital letters. You could probably do this with a clever regular expression search, but saving the formulas and writing a small program might be easier. Cheers, -Eric Eric Martin martine@chiron.com 4560 Horton St., Emeryville, CA 94608 (510)601-3306, FAX (510)601-3360 From mutz@ifp.mat.ethz.ch Mon Apr 24 13:33:14 1995 Received: from bernina.ethz.ch for mutz@ifp.mat.ethz.ch by www.ccl.net (8.6.10/930601.1506) id NAA13089; Mon, 24 Apr 1995 13:19:29 -0400 From: Received: from dove (actually dove.ethz.ch) by bernina.ethz.ch with SMTP inbound; Mon, 24 Apr 1995 19:19:12 +0200 Message-Id: <9504241719.AA14505@dove> Received: from ifp.mat.ethz.ch (erne) by dove.ethz.ch id AA14505; Mon, 24 Apr 95 19:19:27 +0200 Received: by erne.ethz.ch; Mon, 24 Apr 1995 19:20:51 +0200 To: Simon Collins Cc: chemistry@ccl.net, mutz@ifp.mat.ethz.ch Subject: Re: CCL:Charges/bond-breaking In-Reply-To: (Your message of Mon, 24 Apr 95 16:17:13 N.) Date: Mon, 24 Apr 95 19:20:51 +0100 Simon Collins wrote: ------------ Dear All, I am presently interseted in the varience of charge with energy for the heterolytic dissociation of various simple acids, such as HF. I am trying to do this by simply doing single point energies at varying increasing bond lengths, but the molecule splits up homolytically into the radicals. Is there any way round this problem? ------------- Dear Simon, you might do just the opposite of what you did: Start with the separated ions and approach them step by step, instead of breaking up the molecule. Of course, as you approach them, the charge will be redistributed at some point to give more or less the charge distribution of the molecule, but this is what you wanted to model, after all. BTW, there are two different ways to split up a molecule like HF homolytically. The molecule HF in its ground state has all its electrons paired, so it is a singlett. If you separate the two radicals by some distance (e.g. you break the bond), each of the two atoms gets one unpaired electron, and it has to be expected from Hund's rule that the triplett configuration has lower energy. So somewhere midway between the intact molecule and the separated radicals there must be point where the energies of the singlett and triplett state are degenerate in the approximation of Hartree-Fock theory. I don't know about HF, but it might well be that the system undergoes *two* rather than one transition if you move the ions towards each other: Ionic --> Triplett --> Singlett . One last word of caution: The transition point from Triplett to Singlett state is a configuration where there is a large coupling between the movements of the electrons and that of the nuclei (a small movement of the nuclei makes the electron configuration change *qualitatively* !). This means that at this point, one of the most fundamental approximations in electronic structure theory, the Born-Oppenheimer Separation obviously breaks down. It is anything but clear how such systems should be treated (Anybody out there on CCL has any experience in the field, perhaps ? ) Greetings from Zurich -Marcel Utz. ------------------------------------------------------------------------------ Marcel Utz phone: +41 1 632 5672 Institute of Polymers fax: +41 1 632 1096 ETH-Zurich CNB E 98.2 CH-8092 Zurich, Switzerland email: Marcel.Utz@ifp.mat.ethz.ch ------------------------------------------------------------------------------ From shenkin@still3.chem.columbia.edu Mon Apr 24 14:33:00 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id OAA14405; Mon, 24 Apr 1995 14:23:27 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA00866 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Mon, 24 Apr 1995 14:23:18 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@ccl.net id AA23300; Mon, 24 Apr 95 14:23:10 -0400 From: "Peter Shenkin" Message-Id: <9504241423.ZM23298@still3.chem.columbia.edu> Date: Mon, 24 Apr 1995 14:23:02 -0400 In-Reply-To: margot "CCL:Clarification on trivia question" (Apr 24, 3:37pm) References: <0098F5E1.D29ABF26.99@bkfug.kfunigraz.ac.at> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: margot , eslone@osf1.gmu.edu Subject: Re: CCL:Clarification on trivia question Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Apr 24, 3:37pm, margot wrote: > Subject: CCL:Clarification on trivia question > According to "The Name Game" by A. Nickon and E. F. Silversmith, Pergamon > 1987, p. 149 > > a compound containing 10 elements: C60H78Br2CdCl2I2N16O2P2W2 ... > Have fun, > margot OK, Margot, you're on. Here's my idea of fun; YMMV: Let's see; the cited compound has 167 atoms divided among 10 atom types. Certainly this would not be as impressive as a molecule that has 10 atoms, all of different types. But is it as impressive as, say, formamide, which packs four atom types into a molecule with only six atoms? How might one devise an "impressiveness metric" for this problem? Let's define N as the number of atoms and k as the number of atom types. Let us denote by "Metric 0" k itself. One might be tempted to try to use k/N as a metric; this has a maximum of 1 for any molecule that has as many types as it has atoms, but does not accord with intuition, since any monatomic species exhibits this maximum, and we don't regard these as "impressive." Anyway, call k/N Metric 1. A second thought might be to use the product of k and k/N (i.e., k^2/N) as an impressiveness metric. Call this Metric 2. Metric 2 has no theoretical maximum, which is good, since how can one put a maximum on how impressed one can be? After all, if someone comes along tomorrow with a molecule that has 11 types crammed into 167 atoms, we ought to be even more impressed than by Margot's example. How do several molecules compare according to these metrics? Ar CO margot formamide 2*formamide N 1 2 167 6 12 k 1 2 10 4 4 Metric 0 1 2 10 4 4 Metric 1 1 1 0.060 0.67 0.33 Metric 2 1 2 0.60 2.67 1.33 (N.B. 2*formaldehyde is formaldehyde dymer) Note that using Metric 2, formaldehyde is quite a bit more impressive than Margot's example. Note also that both Metric 1 and Metric 2 consider formamide dimer to be less impressive than formamide itself. Let's think about this a bit further, now. In Margot's example, several atom types (Br, Cd, Cl, I, O, P, W) occur only one or two times. In fact, the remaining 30% of the types take up 92% of the atoms. It scarcely seems fair to ascribe full importance to types which appear with very low frequency. We would like to derive a k-value adjusted for frequency of appearance. The information-theoretical (or statistical) entropy provides a way of doing this. First one calculates an entropy as follows: S = - Sum_over_k_types{ p[i] log_B p[i] } where B is the base of the logarithm used and p[i] is n[i]/N, where n[i] is the number of times that type appears; thus, for C in formaldehyde, p[i] is 1/6. We then calculate the "effective number of types" as: k* = B^S. Thus, if the natural log is used in the calculation of S, k* = exp( S ). (We belabor this point because in information theory, it is common to use B=2, giving S in bits. Then k*=2^S. But k* will always come out the same regardless of the base of the log.) k* achieves its theoretical maximum of k when all the types appear equal frequency, but is lower than k when the frequencies of type appearance are unequal. Thus, for CO, k=k*=2, but for Margot's example we have k=10, but k*=3.657. Note that this accords with our notion that only about 3 types account for most of the atoms in this molecule. k* has an interpretation similar to that of the numerical value of a partition function: it is approximately equal to the number of types "occupied" in the molecule; types with small fractional populations don't count for very much. So I define Metric 3 to be simply k*. The results using it are interesting, but share some of the difficulties of Metric 0; namely, if the molecule grows with the same distribution of atoms, as by dimerization, k* doesn't change; we would be more impressed if we could "fill up" the available atoms with types, and k* doesn't reflect this. Nevertheless, note that just using k*, formaldehyde is nearly as impressive as Margot's example. My final proposal, Metric 4, is just like Metric 2, but replacing k with k*; i.e., it is equal to k*^2/N. Results for the four molecules shown above are as follows: Ar CO margot formamide 2*formamide N 1 2 167 6 12 k 1 2 10 4 4 k* 1 2 3.657 3.464 3.464 Metric 0 1 2 10 4 4 Metric 1 1 1 0.060 0.67 0.33 Metric 2 1 2 0.60 2.67 1.33 Metric 3 1 2 3.657 3.464 3.464 Metric 4 1 2 0.080 2.000 1.000 Note that by most reasonable criteria (including Metric 4, the most reasonable, IMHO), formamide is far more impressive than Margot's example. The grand challenge: What is the most impressive molecule you can think of, using Metric 4? Basically, having a lot of types crammed into a small number of atoms will win. For example, CFClBrI has k=k*=5, and Metric 4 = 5. Note that if N=k (all types are different), Metric 4 is equal to k, since in this situation k*=k (all types occur with equal frequency). It probably would be fairly easy for inorganic chemists to come up with compounds for which Metric 4 is 9 or 10. -P. Literature references for k*: 'Information-theoretical Entropy as a Measure of Sequence Variability', Peter S. Shenkin, Batu Erman and Lucy D. Mastrandrea, PROTEINS: Structure, Function and Genetics, 11, 297-313 (1991) Rosemary Swanson also published on the same concept in J. Chem. Ed. She gave the name "optiony" to what I call k*. I'm rather partial to k*; I especially like her duets with Tennessee Ernie Ford. :-) -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From sichelj@Umoncton.CA Mon Apr 24 17:32:59 1995 Received: from bosoleil.ci.umoncton.ca for sichelj@Umoncton.CA by www.ccl.net (8.6.10/930601.1506) id RAA18401; Mon, 24 Apr 1995 17:20:36 -0400 Received: by bosoleil.ci.umoncton.ca (1.37.109.14/16.2) id AA290938474; Mon, 24 Apr 1995 18:21:14 -0300 Date: Mon, 24 Apr 1995 18:21:13 -0300 (ADT) From: John Sichel Sender: John Sichel Reply-To: John Sichel Subject: CCL: trivia and information theory To: Peter Shenkin Cc: margot , eslone@osf1.gmu.edu, chemistry@ccl.net In-Reply-To: <9504241423.ZM23298@still3.chem.columbia.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Peter Shenkin seems to have been carried away by information theory in an attempt to define "impressiveness". I suggest that most chemists would relate "impressiveness" to synthetic difficulty. The latter may not be a quantifiable concept, but we all know that C60 H78 Br2 Cd Cl2 I2 N16 O2 P2 W2 was harder to synthesize than formamide or CFClBrI. So perhaps Eric Slone's simple question actually points to a better _chemical_ measure of impressiveness (number of different elements), even if Peter Shenkin has used more impressive mathematics. Now can anyone beat Margot's molecule with ten different elements? John Sichel Universite de Moncton, Canada > On Apr 24, 3:37pm, margot wrote: > > a compound containing 10 elements: C60H78Br2CdCl2I2N16O2P2W2 On Mon 24 Apr 1995, Peter Shenkin wrote: > Note that using Metric 2, formaldehyde is quite a bit more impressive > than Margot's example. Note also that both Metric 1 and Metric 2 consider > formamide dimer to be less impressive than formamide itself. > Note that by most reasonable criteria (including Metric 4, the most > reasonable, IMHO), formamide is far more impressive than Margot's > example. > > The grand challenge: What is the most impressive molecule you can think > of, using Metric 4? Basically, having a lot of types crammed into > a small number of atoms will win. For example, CFClBrI has k=k*=5, From eslone@osf1.gmu.edu Mon Apr 24 20:03:00 1995 Received: from osf1.gmu.edu for eslone@osf1.gmu.edu by www.ccl.net (8.6.10/930601.1506) id TAA19978; Mon, 24 Apr 1995 19:56:02 -0400 Received: by osf1.gmu.edu; (5.65v3.0/1.1.8.2/07Sep94-1001AM/GMUv1) id AA09328; Mon, 24 Apr 1995 19:56:01 -0400 Message-Id: <9504242356.AA09328@osf1.gmu.edu> Subject: The Winner (thus far) To: chemistry@ccl.net Date: Mon, 24 Apr 1995 19:56:01 -0400 (EDT) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL24alpha5] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1229 The winner thus far is: 15 elements Aluminum barium calcium cerium europium germanium magnesium manganese polonium strontium terbium yttrium chloride fluoride oxide Al 3.56 Ba 0.14 Ca 0.03 Ce 0.11 Cl 0.02 Eu 0.06 F 0.15 Ge 0.15 Mg 0.97 Mn 0.15 O 8.58 Po 0.24 Sr 0.01 Tb 0.07 Y 1.08 Now, for the bonus prize, *what is this compound used for*? and what is it's structure? Please fax your entries to the number shown below. Entires will be judged on originality, artistic ability, and distance travelled. :-) Void where prohibited. The decision of the judges (me) is final. Eric ________________________________________________________________________________ J. Eric Slone George Mason University Department of Chemistry Fairfax, Virginia 22030-4444 Internet: eslone@gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Pager: (202) 597-2373 Miguel de Unamuno Voice: (703) 461-7078 ________________________________________________________________________________