From F66269@VM.BIU.AC.IL Wed Apr 27 04:31:57 1994 Received: from phem3 for F66269@VM.BIU.AC.IL by www.ccl.net (8.6.4/930601.1506) id DAA22930; Wed, 27 Apr 1994 03:58:47 -0400 Received: from VM.BIU.AC.IL (MAILER@BARILVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HBNMJ7R2WW99FHDX@phem3.acs.ohio-state.edu>; Wed, 27 Apr 1994 03:58:37 EDT Received: from VM.BIU.AC.IL (NJE origin F66269@BARILVM) by VM.BIU.AC.IL (LMail V1.2a/1.8a) with BSMTP id 6803; Wed, 27 Apr 1994 10:58:17 +0300 Date: Wed, 27 Apr 94 10:56:32 IDT From: ariel Subject: bill saunders To: chemistry@ccl.net Message-id: <01HBNMJ8K0L299FHDX@phem3.acs.ohio-state.edu> MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT To Bill Saunders! your answer about ab-initio calculation with Argon was very helpfull. thank you very much ariel From jlehmann@ccs.carleton.ca Wed Apr 27 08:31:59 1994 Received: from alfred.ccs.carleton.ca for jlehmann@ccs.carleton.ca by www.ccl.net (8.6.4/930601.1506) id IAA25117; Wed, 27 Apr 1994 08:29:24 -0400 Received: from superior.YP.nobel (superior.ccs.carleton.ca) by alfred.ccs.carleton.ca (4.1/SMI-4.0) id AA03813; Wed, 27 Apr 94 08:29:26 EDT From: jlehmann@ccs.carleton.ca (Jens Lehmann) Received: by superior.YP.nobel (4.1/Sun-Client) id AA03618; Wed, 27 Apr 94 08:27:04 EDT Message-Id: <9404271227.AA03618@superior.YP.nobel> Subject: Polymer Conformation Calculations ? To: CHEMISTRY@ccl.net (Computational Chemistry List) Date: Wed, 27 Apr 94 8:27:03 EDT X-Mailer: ELM [version 2.3 PL11] Hi netters, one of my collegues ask me about the possibilities for MM or AM1 or other empirical or semiempirical calculations of Poly- aryletherketons containing ca. 1000 of the following monomer unit: [-O-Ph-CO-Ph-Ph-CO-Ph-O-Ph-]. He is interested in the preferred conformation(s) of the monomer units in the Polymer. I want to post this question here because I have no real idea how to handle such large molecular structures. Any suggestions are welcome ! Thanks and greetings Dr. Jens Lehmann Dept. of Chemistry, Carleton University Colonel By Drive 1125, Ottawa, Ontario K1S 5B6, Canada Phone: (613) 788-2600 Ext. 3994 e-mail: jlehmann@ccs.carleton.ca From burkhart@goodyear.com Wed Apr 27 09:32:44 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id JAA25740; Wed, 27 Apr 1994 09:09:25 -0400 Received: from rdsrv2 by goodyear.com (4.1/SMI-4.1) id AA19438; Wed, 27 Apr 94 09:09:23 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA11199; Wed, 27 Apr 94 09:09:23 EDT Received: by rds325 (940406.SGI/931108.SGI.AUTO.ANONFTP) for chemistry@ccl.net id AA04843; Wed, 27 Apr 94 09:09:22 -0400 Date: Wed, 27 Apr 94 09:09:22 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404271309.AA04843@rds325> To: chemistry@ccl.net Subject: JOINT MTG CORRECTION Dear Netters: The final schedule that was posted on the net for the First Joint Meeting between the Northeastern Ohio Modeling Interest Group (NEOMIG) and the Pittsburgh Academic and Industrial Modeling Group (PAIMG) had a date error. The agenda stated that MAY 3, 1994 is a FRIDAY. This is an error. The correct day of the week is TUESDAY. The actual date is correct. Sorry for the inconvenience. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From trevor@grserv.wustl.edu Wed Apr 27 12:32:15 1994 Received: from wugate.wustl.edu for trevor@grserv.wustl.edu by www.ccl.net (8.6.4/930601.1506) id MAA07507; Wed, 27 Apr 1994 12:26:12 -0400 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA24900; Wed, 27 Apr 1994 11:26:11 -0500 Received: from giovanni.wustl.edu by grserv via SMTP (920330.SGI/920502.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA02228; Wed, 27 Apr 94 11:29:55 -0600 Received: by giovanni (920330.SGI/920502.SGI) for @grserv:CHEMISTRY@ccl.net id AA10017; Wed, 27 Apr 94 11:29:54 -0600 Date: Wed, 27 Apr 94 11:29:54 -0600 From: trevor@grserv.wustl.edu (Trevor Creamer) Message-Id: <9404271729.AA10017@giovanni> To: CHEMISTRY@ccl.net Subject: Helix dipoles continued Continuing the recent discussion on helix dipoles...... People interested in this may want to have a look at a paper that's just come out : P.Chakrabarti, Protein Engineering v.7(4), p.471-474(1994) The author analyses the distributions of ions bound to the ends of helices in proteins and comes to the conclusion that the helix dipole has little, if any, effect on the ion positions. So, just how important is the dipole ? Cheers, Trevor ________________________________________________________________________ Trevor P. Creamer Dept. of Biochemistry Email - trevor@grserv.wustl.edu & Molecular Biophysics Phone - (314) 362 4123 Washington University Fax - (314) 362 4115 St. Louis, Missouri 63110 U.S.A. ________________________________________________________________________ From C1790@SLVAXA.UMSL.EDU Wed Apr 27 13:31:59 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id MAA07717; Wed, 27 Apr 1994 12:37:54 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HBO2ERY1TS9ZMVWK@SLVAXA.UMSL.EDU>; Wed, 27 Apr 1994 11:38:31 CST Date: Wed, 27 Apr 1994 11:38:31 -0600 (CST) Subject: CALCULATION OF pKa's To: CHEMISTRY@ccl.net Message-id: <01HBO2ES1J829ZMVWK@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, DOES ANYONE KNOW OF A QSAR OR GROUP-ADDITIVITY TYPE METHOD FOR PREDICTING (i.e., CALCULATING) pKa's. FOR EXAMPLE, I THOUGHT THERE WAS A HANSCH-LIKE DATABASE PROGRAM FOR MAKING SUCH PREDICTIONS BUT I'M NOT SURE. THANKS MUCH ... BILL WELSH UNIV. OF MISSOURI-ST. LOUIS CHEMISTRY DEPT. From mrigank@imtech.ernet.in Wed Apr 27 13:34:48 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.4/930601.1506) id MAA07807; Wed, 27 Apr 1994 12:42:55 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id WAA06442 for chemistry@ccl.net; Wed, 27 Apr 1994 22:12:36 +0530 Received: from imtech.UUCP by ern.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA27207; Wed, 27 Apr 94 21:48:03+0530 Message-Id: <9404271618.AA27207@ern.doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Wed, 27 Apr 94 21:36:12 +0530 Date: Wed, 27 Apr 94 21:36:12 +0530 From: "Dr. Mrigank" To: chemistry@ccl.net Subject: Why no start a usenet news group ? X-Vms-Mail-To: CHEM,AMBER,WATOC,MRIGANK Hi Why do not one start this list also as USENET newsgroup. Like sci.chemistry.computational s.c.c.amber and so on. To start with s.c.c and then expand. This can be done simultaneuosly if JL willing. just a suggestion. Mrigank ---- Dr. Mrigank \/Phone +91 172 45004 x216, +91 172 44252 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\Fax +91 172 40985 or +91 172 603903 ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From elewars@alchemy.chem.utoronto.ca Wed Apr 27 13:35:56 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id MAA07802; Wed, 27 Apr 1994 12:42:37 -0400 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id MAA11940 for chemistry@ccl.net; Wed, 27 Apr 1994 12:41:47 -0400 Date: Wed, 27 Apr 1994 12:41:47 -0400 From: "E. Lewars" Message-Id: <199404271641.MAA11940@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: symmetry and stationary points Patrick Bultinck started a discussion about whether or not symmetry constraints should be used in calculations. When we do a geometry optimization we're seeking a stationary point (which almost alwars means a relative minimum or a transition state). Since it's sound practice to characterize any stationary point you have found by calculating its freqs, it is probably a good idea to routinely impose symmetry (for esthetic reasons and to save time) and let the number of imaginary vibrations tell you when to relax it to go from a transition state to a minimum. Theresa Windus says "while the molece with symmetry may not be the global minimum...it is certainly some sort of stationary point..." Does anybody know of a formal theorem that says non-C1 structures are always stationary points, or some place where this is explicitly stated? It's just that it would be nice to see some sort of proof; it's not quite obvious that it MUST be so, altho' I do see that it looks reasonable. Thanks. === From dwelrod@intnet.upj.com Wed Apr 27 14:32:07 1994 Received: from intnet.upj.com for dwelrod@intnet.upj.com by www.ccl.net (8.6.4/930601.1506) id OAA09420; Wed, 27 Apr 1994 14:09:17 -0400 From: Received: by intnet.upj.com (5.67/2.25) id AA12520; Wed, 27 Apr 94 23:41:28 GMT Received: by intnet.upj.com (5.67/2.25) id AA07140; Wed, 27 Apr 94 23:41:23 GMT Message-Id: <9404272341.AA07140@intnet.upj.com> Date: Wed, 27 Apr 94 23:41:23 GMT To: chemistry@ccl.net Subject: ChemRXS Chemical Design's Reaction searching software Cc: dwelrod@upj.com Also posted to CHEMINF-L Does anyone have actual experience with Chemical Design's ChemRXS reaction searching program? If appropriate, reply to me instead of to CCL. I will post a summary, with the sender's permission if there is sufficient information of general interest. Thanks, Dave Elrod dwelrod@upj.com From jxh@ibm12.biosym.com Wed Apr 27 14:33:39 1994 Received: from ibm12.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.4/930601.1506) id OAA13332; Wed, 27 Apr 1994 14:18:56 -0400 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA21186; Wed, 27 Apr 1994 11:18:27 -0700 Date: Wed, 27 Apr 1994 11:18:27 -0700 From: jxh@ibm12.biosym.com (Joerg Hill) Message-Id: <9404271818.AA21186@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:symmetry and stationary points E. Lewars wrote: > [ ... ] > Theresa Windus says "while the molece with symmetry may not be the global > minimum...it is certainly some sort of stationary point..." Does anybody > know of a formal theorem that says non-C1 structures are always stationary ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > points, or some place where this is explicitly stated? It's just that it ^^^^^^ If you OPTIMIZE your molecule under the restriction of a specific point group and you find a point where all force vanish you have found a stationary point (that's how stationary points are defined). So it doesn't matter whether the molecule possesses symmetry or not at this point of its potential surface. > would be nice to see some sort of proof; it's not quite obvious that it > MUST be so, altho' I do see that it looks reasonable. But the probability that you have found a MINIMUM is very small. In most cases you will found one or even more imaginary frequencies and you have to optimize further using a subgroup of your current point group (C1 is a always a subgroup) and starting with a distortion of your current geometry (preferably along a normal mode with an imaginary frequency), since otherwise you stay at your current stationary point of the potential surface (there are no force your optimizer can minimize). Using symmetry makes sense if you know from experiment that your molecule belongs to a special point group or your chemical intuition tells you that symmetry may play a role. Use of symmetry for speeding up or making calculations possible has always to be considered as giving you wrong answers (no minima). If your molecules are models for larger systems and the imaginary frequencies affect only parts of the molecule which are not present in your larger system, you may use symmetry, too. Joerg-R. Hill From rgab@purisima.molres.org Wed Apr 27 14:34:39 1994 Received: from purisima.molres.org for rgab@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id NAA08322; Wed, 27 Apr 1994 13:33:50 -0400 Message-Id: <199404271733.NAA08322@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA04478; Wed, 27 Apr 94 10:14:17 -0700 Date: Wed, 27 Apr 94 10:14:17 -0700 From: "R.G.A. Bone" To: chemistry@ccl.net Subject: Symmetry: In Reply to Dan Severence In reply to Dan Severence's comments: i) Gaussian calculations. >> "Gaussian" finds symmetry present in the input nuclear coordinates and >> applies it unless you explicitly switch it off. But geometry optimizations >> will typically, irritatingly, quit as soon as a change in point group occurs. > > If you wish to force the symmetry, this can be averted by using the >same variable name for the symmetric lengths and angles, thus there is >no possibility of a change in point group. > Yes, Dan is correct, provided that you can do it. Constraining the internal coordinates in the Z-matrix is the way out. But I had one fiendish example once (in "C_i" symmetry) where it was not possible to do this: two related angles could not be specified by the same internal coordinate and the optimization failed as soon as these angles became slightly inequivalent. ii) I was very careful in my comment about the gradient. >> The gradient of the energy w.r.t. nuclear displacements should transform as >> the totally symmetric 'irrep' in whatever point group you happen to be in. >>For 'closed-shell' systems (no electronic degeneracies) this means in practice >> that 'symmetric' structures are usually stationary points. The only > > There are actually a number of cases where this is indeed not the > case. Amides, for instance, tend not to be planar but are slightly > puckered at the N. It often doesn't take much energy to force it to > be planar, but non-planar is the minimum at any levels of theory that > I've seen. Also, quite bulky molecules often avoid a symmetric > form in favor of spreading out the steric interactions. > Note that I said that symmetric structures are usually STATIONARY POINTS, not 'MINIMA'. Nothing I said contradicted the example of a non-planar amide. But, symmetry can not be interpreted to be 'local' either. I was about to venture that the configuration in which the bonds about the N-atom are planar would probably be a 'transition state' but of course such a structure may not be a stationary point at all if there are other 'out-of-plane' atoms in the molecule which are not related to one another by reflection in the plane. (Remember those non-bonded interactions ...). If the _whole_ molecule is planar or has a plane of symmetry then (if closed-shell, and in the absence of totally symmetric distortions) it will be a stationary point but I couldn't tell you, a priori, what sort. N.B., Just because symmetric structures are usually stationary, does not mean the converse, either, viz: stationary points do not have to be 'symmetric'. There are clearly a number of pitfalls and potential confusions in the discussion of symmetry. I will shortly post a useful reference-list to CCL which not only provides background to my own comments but should hopefully be a useful almanac to anybody with an interest in this field. Watch this space ......... Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org From rgab@purisima.molres.org Wed Apr 27 15:32:01 1994 Received: from purisima.molres.org for rgab@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id OAA15112; Wed, 27 Apr 1994 14:44:12 -0400 Message-Id: <199404271844.OAA15112@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA04823; Wed, 27 Apr 94 11:24:39 -0700 Date: Wed, 27 Apr 94 11:24:39 -0700 From: "R.G.A. Bone" To: chemistry@ccl.net Subject: USENET News Group ... NO! Why not start CCL as a USENET NewsGroup ... ? ... because, even in 1994, there are still some of us who cannot access "USENET" (or, WWW, etc.) and for whom, therefore, a listserver like CCL is the only lifeline. Many people in companies are behind so-called "firewalls" in which full internet-access (except e-mail) is denied. There are many others in the situation of being in a very _small_ set-up where the capability to install the appropriate protocols (NNTP servers, etc.) does not exist and where the demand is sufficiently low that it is not thought 'worthwhile'. In these situations, e-mail and FTP are the _only_ ways. For those in any of those positions probably the only practical solution is to go through a 'server' like CRL or Netcom and pay, either on a private basis (i.e., at home!) or on a stand-alone machine in the lab. I know that it should be regarded as ironic that scientists/researchers should have to go to such lengths, but it is not unknown. Richard Bone From davis@nod.bms.com Wed Apr 27 15:33:26 1994 Received: from CLIFF.BMS.COM for davis@nod.bms.com by www.ccl.net (8.6.4/930601.1506) id PAA16370; Wed, 27 Apr 1994 15:23:35 -0400 Received: from nod (nod.bms.com) by cliff.bms.com (PMDF #2529 ) id <01HBOAG8RUYO0005IE@cliff.bms.com>; Wed, 27 Apr 1994 15:23:24 EST Received: by nod (920330.SGI/920502.SGI) for @cliff.bms.com:chemistry@ccl.net id AA05005; Wed, 27 Apr 94 15:23:01 -0400 Date: 27 Apr 1994 15:23:01 -0400 From: davis@nod.bms.com (Malcolm Davis) Subject: Re: CCL:Helix dipoles continued In-reply-to: <9404271729.AA10017@giovanni> (trevor@grserv.wustl.edu) To: trevor@grserv.wustl.edu Cc: chemistry@ccl.net Message-id: <9404271923.AA05005@nod> X-Envelope-to: chemistry@ccl.net Content-transfer-encoding: 7BIT The "helix dipole" with 1/2 a charge unit at one end of the alpha helix and -1/2 at the other, yielding a dipole moment of L/2, looks like a dipole only at distances much larger than L. Since, most of the interesting stuff happens at distances much shorter than this the dipole part of the helix dipole is probably not significant. At nearer distances, it still might be useful to view the helix as producing a charge separation, so that near each end you see the field of a net charge, but even this can be led to incorrect conclusions by ignoring the local variation in the fields very near the helix. Consider how such an approximation can lead to an incorrect conclusion in a simple model system. At large separations, a linear chain of dipoles +:- +:- +:- +:- will look like a "macrodipole" + - If one then asks about the interaction with a similar parallel strand, the macrodipole view + - + - would lead one to conclude that the interaction is very unfavorable, but the detailed view +:- +:- +:- +:- +:- +:- +:- +:- shows that the interactions are not so bad after all. -- Malcolm E. Davis USMail: Macromolecular Modeling Email : davis@nod.bms.com Bristol-Myers Squibb Phone : 609-252-4324 P.O.Box 4000 FAX : 609-252-6030 Princeton, NJ 08543-4000 Office: LV H.3812 From ifm.oos@macpost.lidac.liu.se Wed Apr 27 16:34:56 1994 Received: from mailgw.liu.se for ifm.oos@macpost.lidac.liu.se by www.ccl.net (8.6.4/930601.1506) id PAA16790; Wed, 27 Apr 1994 15:41:19 -0400 Received: from macpost.lidac.liu.se by mailgw.liu.se with SMTP (5.61-bind 1.2+ida/IDA-1.2.8.2/LTH) id AA26213; Wed, 27 Apr 94 21:39:09 +0200 Subject: symmetry again To: CHEMISTRY@ccl.net From: Anton van Oosten Date: Wed, 27 Apr 94 21:41:20 +0100 Message-Id: <940427.214120.27577@macpost.lidac.liu.se> Dear netters Here's my two ore contribution to the symmetry discussion. The goal of a calculation is to get a physically relevant result. Therefore the use of absolute symmetry restrictions should be scientifically motivated. Of course, it is usually a good approach to start with a high symmetry and then step by step relax the restrictions. This will economize resources and may at the same time give meaningful information about saddle points. Frequency calculations in principle involve quite a lot - something like n*(n-1)/2 for n degrees of freedom - of lower symmetry calculations, involving all possible pairs of displacements of individual atoms. That may be too much effort, since a check for saddle points requires only n such calculations - or less if bond stretching is avoided. Thanks for your bandwidth ... From jkl@ccl.net Wed Apr 27 16:40:23 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id PAA17110; Wed, 27 Apr 1994 15:59:36 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id PAA02752; Wed, 27 Apr 1994 15:59:34 -0400 Date: Wed, 27 Apr 1994 15:59:34 -0400 Message-Id: <199404271959.PAA02752@krakow.ccl.net> To: chemistry@ccl.net Subject: Re: Why not start a usenet newsgroup now Cc: jkl@ccl.net Dear Compchems, Dr. Mrigank" writes: >Why do not one start this list also as USENET newsgroup. Like >sci.chemistry.computational >s.c.c.amber >and so on. To start with s.c.c and then expand. This can be done simultaneuosly >if JL willing. Before it unfolds any further (I understand that Bionet will be having a newsgroup on molecular modeling) let me tell you why I am so conservative. And if you think that I am too conservative, the CCL will migrate to another place, since I have no way of keeping you here by force {:-)}. And if you unsubscribe, nobody will call you or beat you up {;-0}. Please, do not forget that you can view CCL in a similar way as you do Usenet, by using gopher. So if e-mail is too burdensome for you, you can always do: gopher www.ccl.net 73 archived-messages 94 04 27 and scan messages for the given day. And you do not need to be a subscriber to post to chemistry@ccl.net (at least not now). And if you abuse it, I will prevent you from posting (my infamous "black list"). First, it is technically trivial to interface mailing list with a Usenet group. Why I am not doing it? I read ocassionally several unmoderated Usenet groups. What I find is that they are very noisy. I know that Computational Chemistry List is also noisy, but I still hope that it is less noisy than many other unmoderated groups I have seen. I still have a power to prevent people from posting, if they abuse the list intentionally. I am in the process of preparing a proposal for the support of CCL. I have several things in mind: 1) Splitting CCL into topics (but you will be able to subscribe to all topics if you want) 2) Moderating, i.e., each message will be first reviewed before it is sent to the distribution. I want to provide a multicenter/multi-time-zone and anonymous moderation. This needs some software development. Why? Since I want to keep the interactive "touch and feel". 3) Enhancing archives, their searching, their contents and access. 4) Actively seek good material for the archives. 5) Provide "chemist on duty" to answer trivial questions and other things. Only when I am done with it, I will provide access to CCL via Usenet. You may say, why not today? The answer is, I do not have resources to do it. I know that you have a lot of ideas how to improve the list. But please fight the urge of flooding the list with the discussion about the list. Please, send your ideas to me, and be sure that I will use them if and when I can. I prefer that we keep talking about Computational Chemistry rather than CCL. At some point I may ask you for your help and letters of support. Your "coordinator" Jan Labanowski jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From Bohdan.Szymanik@vuw.ac.nz Wed Apr 27 18:32:03 1994 Received: from kauri.vuw.ac.nz for Bohdan.Szymanik@vuw.ac.nz by www.ccl.net (8.6.4/930601.1506) id RAA18521; Wed, 27 Apr 1994 17:49:54 -0400 Received: by kauri.vuw.ac.nz id AA07322 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 28 Apr 1994 09:48:55 +1200 Date: Thu, 28 Apr 1994 09:48:55 +1200 From: B Szymanik Message-Id: <199404272148.AA07322@kauri.vuw.ac.nz> To: chemistry@ccl.net Subject: Usenet/mailing list A CCl newsgroup from the mailing list...? Why not. We get a lot of the bitnet mailing lists reflected as newsgroups here at Victoria uni. Why couldn't both the list continue as well as a newsgroup? -Bohdan Szymanik Victoria University of Wellington, Industrial Research Ltd From ilya@lisboa.ks.uiuc.edu Wed Apr 27 19:32:04 1994 Received: from lisboa.ks.uiuc.edu for ilya@lisboa.ks.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id TAA18950; Wed, 27 Apr 1994 19:03:57 -0400 Received: from sofia by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA20568; Wed, 27 Apr 94 18:03:51 -0500 From: Ilya Logunov Message-Id: <9404272303.AA20568@lisboa.ks.uiuc.edu> Received: by sofia.ks.uiuc.edu (NX5.67d/NX3.0X) id AA02419; Wed, 27 Apr 94 18:03:50 -0500 Date: Wed, 27 Apr 94 18:03:50 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY@ccl.net Subject: ZINDO Dear Netters, Could somebody give me information about the latest available version of ZINDO (both academic and commercial codes). I also would like to know the coordinates (including a phone number) of professor Zerner, the original creator of ZINDO. Thank you very much in advance ********************************************************* Ilya Logunov Theoretical Biophysics Group Department of Chemistry and Beckman Institute University of Illinois at U-C ilya@ks.uiuc.edu ********************************************************* From rs0thp@RohmHaas.Com Wed Apr 27 20:32:04 1994 Received: from monte.br.RohmHaas.Com for rs0thp@RohmHaas.Com by www.ccl.net (8.6.4/930601.1506) id UAA19391; Wed, 27 Apr 1994 20:00:49 -0400 Received: by monte.br.RohmHaas.Com (AIX 3.2/UCB 5.64/4.03) id AA15862; Wed, 27 Apr 1994 19:59:52 -0400 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9404272359.AA15862@monte.br.RohmHaas.Com> Subject: Re: CCL:Polymer Conformation Calculations ? To: jlehmann@ccs.carleton.ca (Jens Lehmann) Date: Wed, 27 Apr 1994 19:59:51 +22305458 (EDT) Cc: chemistry@ccl.net In-Reply-To: <9404271227.AA03618@superior.YP.nobel> from "Jens Lehmann" at Apr 27, 94 08:27:03 am X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1371 Previously, Jens Lehmann wrote: > One of my collegues ask me about the possibilities for MM or > AM1 or other empirical or semiempirical calculations of Poly- > aryletherketones containing ca. 1000 of the following monomer > unit: [-O-Ph-CO-Ph-Ph-CO-Ph-O-Ph-]. He is interested in the > preferred conformation(s) of the monomer units in the Polymer. > Dear Jens Lehmann, Commercial Polymer Modeling Codes such as BIOSY's, Tripos's or MSI's should be able to answer the question if you believe (as I do) that the conformations are from the same distributions as those measured for smaller chains. A degree of polymerization that results in at least 4-5 Kuhn segment lengths or around one-half the entanglement monomer length should be sufficient. I would guess that about 100 to 200 monomers would be enough and simulated annealing Monte Carlo or simulated annealing Molecular Dynamics calculations would give a very good answer using Molecular Mechanics. It will however, take alot (weeks?) of computer time.. If you have a small entanglement length ( ie a low characteristic ratio - almost a random walk..) You could get by with sampling a 30-40 monomer chain. You would just have more end effects then.. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company."