From anthony.scott@anu.edu.au Fri Oct 22 09:37:04 1993 Date: Fri, 22 Oct 93 14:37:04 EST From: anthony.scott@anu.edu.au (Anthony P Scott) Message-Id: <9310220437.AA22214@cscgpo.anu.edu.au> To: CHEMISTRY@ccl.net Subject: RASMOL2.0 Hello, We have downloaded RasMol2.0 to an IBM/RS6000 355. Some of the routines compile except for the x11win.c which crashes. Has anyone had experience in getting RasMol2.0 to work on this model IBM? If so, either mail to me directly or post here I suppose (although after the fuss last week I am not sure whether a reply to osc is within the guidelines. At any rate thanks for your replies in advance. regards, Tony Scott Research School of Chemistry Australian National University Canberra, ACT, Australia From m10!frisch@uunet.UU.NET Fri Oct 22 01:03:55 1993 Message-Id: <9310221030.AA12356@relay1.UU.NET> Date: Fri, 22 Oct 93 05:03:55 EDT From: m10!frisch@uunet.uu.net (Michael Frisch) Subject: Re: GAUSSIAN 92 printing integrals To: chemistry@ccl.net Does anyone know of a setting in G-92 which allows one to have the integral values (i.e. exchange, coulomb, overlap) printed within the output file? (It's a small molecule, don't worry.). Thanks a lot, Rob ============================================================================= schurko@ccu.umanitoba.ca Robert Schurko Chemistry Department (204)-474-9335 University of Manitoba Winnipeg, MB, CANADA ============================================================================= This is easy but not well documented. Just add "ExtraLinks=L316" to your route. This link prints the integrals in a readable format. Note a) you'll get the raffenetti combinations by default, so say NORAFF as well if you want to see the regular integrals. b) The integrals may have scale factors in them for use of symmetry; say SYMM=NOINT or NOSYMM to avoid this. Mike Frisch ------- From cqsimpson@halnet.com Fri Oct 22 02:13:15 1993 Date: Fri, 22 Oct 1993 07:13:15 -0500 From: cqsimpson@halnet.com (Charlie Simpson) Message-Id: <9310221213.AA14081@cre2> To: chemistry@ccl.net Subject: Bob Harmon's request Corel Draw is an excellent program for making slides. I would definitely check it out. Regards, Charlie Simpson ================================================================================ Charlie Simpson Ph.D. cqsimpson@halnet.com Halliburton Energy Services P.O. Box 1431 Phone 405/251-4564 Duncan, OK 73536-0438 Fax 405/251-3218 A lot of people die at 40, but aren't buried until 30 years later. -- General George S. Patton No one is politically correct who is morally wrong. ================================================================================ From jpj@lotus.medicine.rochester.edu Fri Oct 22 13:44:41 1993 Date: Fri, 22 Oct 93 13:44:41 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) Message-Id: <9310221344.AA02227@lotus.medicine.rochester.edu> To: CHEMISTRY@ccl.net Subject: X-windows terminal emulation DOS? Hello: Could anuone send me information on a PC based X-windows emulation package. I'm interested in using the PC as a terminal for SYBYL. $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Jeffrey P. Jones Ph.D Assistant Professor of Pharmacology University of Rochester 601 Elmwood Ave. Rochester, NY 14642-8411 (716)275-5371 jpj@lotus.medicine.rochester.edu $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ THE ONLY EXISTING THINGS ARE ATOMS AND EMPTY SPACE; ALL ELSE IS MERE OPINION. -- DEMOCRITUS OF ABDERA D. 370 B.C. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From fredvc@esvax.dnet.dupont.com Fri Oct 22 05:49:30 1993 Date: Fri, 22 Oct 93 09:49:30 -0400 Message-Id: <9310221349.AA14054@esds01.es.dupont.com> From: fredvc@esvax.dnet.dupont.com To: chem@ccl.net Subject: RE: VIBRATIONAL ANALYSIS Sorry to consume bandwidth, but I mislaid the e-mail address of the person asking questions about vibrational analysis. In order to do vibrational analysis, you have to have the full second derivative matrix for the energy. "Brute force" evaluation of this matrix numerically requires ~N(N+1)/2 energy evaluations. A good description the numerical approach to second derivative evaluations in general can be found in Bevington's "Data Reduction and Error Analysis for the Physical Sciences", Section 11-3. It's relevance to the vibrational analysis problem should be clear. The step size used (Cartesian coordinates) in the ab initio MO program GAMESS is 0.01 Bohr (~0.0053 Angstroms). I hope this is helpful. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From adit@Kodak.COM Fri Oct 22 05:40:30 1993 Date: Fri, 22 Oct 93 09:40:30 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9310221340.AA19656@bcc9.kodak.com> To: chemistry@ccl.net Subject: Reminder for electronic posters. ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 12 Hi Folks, Just a quick reminder that the deadline for contacting me if you want to submit an electronic poster at the upcoming MM/MD workshop (see attachment) is fast approaching. It is October 30! If you are thinking of doing it but don't have the whole poster ready yet THAT's OK. I just need to know. Thanks. Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com ---------- X-Sun-Data-Type: sun-deskset-message X-Sun-Data-Name: sun-deskset-message X-Sun-Encoding-Info: uuencode X-Sun-Content-Lines: 99 begin 600 sun-deskset-message M1G)O;2!C:&5M:7-T2U4;SH@861I=$!K;V1A:RYC;VT*1&%T93H@36]N M+" T($]C=" Y,R Q-3HU,3HT,B!%1%0*1G)O;3H@861I=$!K;V1A:RYC;VT@ M*$%D:2!47=A;&$I"E1O.B!C:&5M:7-TG5I:RP@1G)A;FL@3&5U6YA M;6EC6YA;6EC M&AI M8FET6UE;G0@*&-H96-K2D@=&\Z("!#;VYF97)E;F-E(%)E9VES=')A M2P@5&%L;&%H87-S964@1DP@(#,R,S V+3(P,C6]U(')E<75I6UE;G1S+@H*"@H*"BTM+0I!9&UI;FES=')I M=FEA.B!4:&ES(&UE2!A<'!E;F1E9"!B M>2!T:&4@;6%I;"!E>'!L;V1E Date: Fri, 22 Oct 1993 16:34:05 +0100 To: chemistry@ccl.net From: NMUELLER@edvz.uni-linz.ac.at (Norbert Mueller) Subject: HyperChem 3.0 for SGI Would anyone more knowledgeable than myself please comment on the rumour that AutoDesk will drop HyperChem for the SGI - meaning that there will not be a version 3.0 for SGI. -- Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at (MacPost) NorbertM (AMDA-Link Linz) <-FirstClass NorbertM@AMDA.UNI-LINZ.AC.AT ->FirstClass From hogue@denmark.den.mmc.com Fri Oct 22 04:29:01 1993 Date: Fri, 22 Oct 93 10:29:01 MDT From: hogue@denmark.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9310221629.AA01328@denmark.den.mmc.com> To: chemistry@ccl.net Subject: Radical HOMO/LUMO Dear Netters: I'm coming up on a MS thesis defense and could appreciate any dear souls willing to consider whether I am interpreting my results correctly, especially the radical. As near as I can tell there are four ways a linear perfluoropolyether molecule can decompose on a surface: 1. Lewis acid complexation with ether oxygens, resulting in trans-oxygen fluorine transfer, molecular disproportionation and subsequent thermally induced decomposition of fluorofomate to F2CO gas. The Lewis acid could be Al2O3. This is Paul Kasai's mechanism. 2. Lewis acid abstraction of fluorine through attack on F lone pairs to leave a cation which can be stabilized by resonance with ether oxygens, this is especially likely for an acetal (-O-CF2-O-) group. Subsequent depolymerization can also release the F2CO gas always found experimentally. The Lewis acid FeF3 fills this bill. D. Carre, W. Jones, M. Zehe and O. Faut mechanism. 3. Bronsted acid attack on ether oxygen, presumably to cleave the bond and result in some kind of surface bound species and alcohol fragment. Gama Fe2O3 works here. W. Morales (NASA, Lewis). 4. Nucleophillic (electron donation) on fluorine, resulting in abstraction of F- leaving a polymer radical that undergoes radical depolymerization, also releasing F2CO. This mechanism probably operates on bare metal (Al, Fe) surfaces. (P. Stair, M. Napier) My thesis only looks at mechanisms 2 and 4. I recently modelled a small perfluoropolyether with the following formula (CF3OCF2OCF2CF2)2O using AM1. I then removed one fluorine (mechanism #2 above) near the center of the molecule (one of the F's participating in the HOMO) to simulate abstraction by a Lewis acid, this left a polymer cation. The HOMO shifted from the center of the molecule to three terminal fluorines at one end of the cation and the oxygen adjacent to them (it had a big coefficient). I take this result to mean that this trifluoromethoxy group is ready to leave with the next available Lewis acid site. Does the Net agree? Next I abstracted a F- to leave a polymer radical (mechanism #4 above). The HOMO was delocalized over the whole molecule (except for the oxygen that had the high HOMO coefficient in the cation described above). The LUMO was delocalized as well, but not quite to the extent the HOMO was. The terminal oxygen did participate in this LUMO. This radical case is a little harder for me to make sense of. The radical had both HOMO and Lumo coefficients on sigma orbitals. Cation case HOMO/LUMO orbitals were associated with p orbitals only. Does the involvement of sigma orbitals in the radical case signal incipient fragmentation? Or is the radical content to simply delocalize the odd electron and float in the vacuum for ever? It certainly seems like another electron would break a bond. I didn't model this though. 10e6 thanks to all who are willing to offer (helpful) comments. Pat Hogue From h.rzepa@ic.ac.uk Fri Oct 22 17:28:26 1993 Message-Id: <9310221729.AA21803@cscmgb.cc.ic.ac.uk> Date: Fri, 22 Oct 1993 17:28:26 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: ACD Gopher and Group 4 Fax Compression I am having difficulty reading the TIFF images on the ACS Gopher. I have tried both JPEG Viewer 3.0 and GIFConverter 2.3.1 on a Macintosh, but neither supports the G4 Fax compression. The ACS readme says "The following list contains a sample of some of the commercial, shareware, and public-domain packages which can be used to display TIFF images. Note that some of the packages can not currently handle Group 4 Fax compression within TIFF files. For those packages, additional graphics file conversion software will be needed to uncompress the images before they can be displayed. " It does not say which of the Mac packages cited (all commercial software, and some of it quite expensive, ie Quark) need the "additional software" to decompress the files. Nor does it say what that additional software might be. I have trawled far and wide, and no-one here in the UK I have asked has any idea what Mac programs might do this. Now, why did they chose such a difficult format? Commercial reasons no doubt! Can anyone help? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From mgauss@alchemy.chem.utoronto.ca Fri Oct 22 11:37:27 1993 Date: Fri, 22 Oct 93 15:37:27 -0400 From: mgauss@alchemy.chem.utoronto.ca (Mike Peterson / Monstergauss) Message-Id: <9310221937.AA11672@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Re: GAUSSIAN 92 printing integrals After Mike Frisch explained how to get the 2-e ints printed, here is the command line I am using (for our ab initio course) which prints almost everything there is: #p pop=full test gfprint iop(3/33=1,3/36=1) extralinks=l316 noraff nosymm guess=print scf=nodirect Iop(33) means to print the 1-e ints, Iop(36) limits the multipole ints to dipole (x/y/z). You need either the programmers manual or to look at the l301.F file to get all this info. Mike. From lozano@farmacia.ub.es Fri Oct 22 17:09:50 1993 Message-Id: <199310222020.AA12226@oscsunb.ccl.net> From: Joan_Josep Lozano Salvatella Subject: SUBSCRIBE_PLEASE!!! To: CHEMISTRY@ccl.net Date: Fri, 22 Oct 93 21:09:45 MET HELLO!! Please Susbcribe email lozano@farmacia.ub.es unitat de fisico-quimica Facultat de Farmacia universitat de Barcelona Barcelona Spain Thanks From jkl@ccl.net Fri Oct 22 12:51:49 1993 From: Jan Labanowski Date: Fri, 22 Oct 1993 16:51:49 -0400 Message-Id: <199310222051.AA21633@krakow.ccl.net> To: chemistry@ccl.net Subject: FAQ and LIST STOPPED Dear Netters, This is your coordinator speaking. WAIT TILL MONDAY BEFORE SENDING ANYTHING TO THE LIST OR ME !!! And please, read the rest of this message. I told you last Sunday that we (i.e., Ohio Supercomputer Center) are moving to the new machine for mailing, gopher, ftp. This will be a major disaster. It will require changing many installation files, etc., and then checking if everything works. It will also affect all my scripts running the list, and all other services. However, as a result, the mail will be distributed much faster. Also, the archives moved from the NFS mounted disks to the disks on the mailer. Therefore archive searches will be at least 5 times faster. So, the list will be shut down today and not available through the weekend. Do not even attempt to send anything to it, since it will probably be lost. Wait for the message from me which resumes the list operation. Now about the file with FAQ (Frequently Asked Questions). Let me start from this. I DO NOT WANT ANY OPEN DISCUSSIONS ABOUT IT ON THE LIST. PLEASE ADDRESS ALL COMMENTS TO ME, AND I WILL RELAY THE INFORMATION TO THE LIST ABOUT THE PROGRESS (OR LACK OF IT). Few explanations. The FAQ is a popular jargon term denoting the file which collects questions and answers to frequently asked questions on a given list or newsgroup. Such files are available on some anonymous ftp and availability of FAQ is announced to the list/newsgroup periodically. This is done to limit the noise on the list. We all know how many times we have seen questions: What is QCPE? Where to get MOPAC? How to find an ftp site with program XXX? Where to find intro in MM?, What software for X on PC, etc. I want to share some thoughts on this: 1) FAQ will be an ongoing, constant effort to expand, correct and update the file. I will coordinate it, but can only contribute to these portions of FAQ which I feel familiar with. So it will be a joint project, and I AM ASKING FOR YOUR HELP. 2) We will not have the FAQ tomorrow. It takes time and effort to produce one. Bad FAQ produces more questions than it answers. 3) Due to the breadth of the topic, I do not see a FAQ as a selfcontained single file. I see it rather as questions, very short definitions, and pointers to a document/file in our archives. We already have many short notes and pieces of information there. It is time to update them and point to them. 4) There are already many, many messages on the list, which can be a good seed (or even perfect final product) for the FAQ entry. At this moment, I would ask you for suggestions on what should be included in the FAQ. Please write TO ME ONLY. After I compiled your suggestions, I will present them to the list, and at this time ask for your contributions. We may also create a small list for people who want to work with me on this project, but I do not want to force anything on anybody. If you want to help and got a spare hour, you are welcome. If you are busy, I will understand this perfectly, and will "let you go without any questions asked". I also invite software developers to provide information about their products, addresses, whatever. I ask everybody to contribute whatever they can. If not answers than questions... Why we are doing this? BECAUSE it is good for our students. And we owe this to them. And if you do not believe this one, then we do it for ourselves, to popularize a discipline which is neither easy, nor popular. Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From mckelvey@Kodak.COM Fri Oct 22 15:15:47 1993 Date: Fri, 22 Oct 93 19:15:47 -0400 Message-Id: <9310222315.AA06612@Kodak.COM> From: mckelvey@Kodak.COM To: osc@Kodak.COM Subject: The best mother-board/processor for heavy stuff on PC ? Which PC mother-board/processor is best for G92W, MOPAC, etc..? 1) EISA with 66mhz/DX2 2) ISA with 66mhz/DX2 3) EISA with 50mhz/DX (not DX2) 4) others WHY ? I will post summary. Thanks in advance!! John McKelvey Eastman Kodak