From uko@ufark2.chem.ufl.edu Fri Jan 19 10:20:13 1996 Received: from nervm.nerdc.ufl.edu for uko@ufark2.chem.ufl.edu by www.ccl.net (8.6.10/950822.1) id KAA11301; Fri, 19 Jan 1996 10:19:32 -0500 Received: from ufark2.chem.ufl.edu by nervm.nerdc.ufl.edu (IBM VM SMTP V2R3) with TCP; Fri, 19 Jan 96 10:19:05 EST Received: by ufark2.chem.ufl.edu (AIX 3.2/UCB 5.64/4.03) id AA03031; Fri, 19 Jan 1996 10:23:29 -0500 From: uko@ufark2.chem.ufl.edu (Uko Maran) Message-Id: <9601191523.AA03031@ufark2.chem.ufl.edu> Subject: Room mate for Sanibel Symposium To: chemistry@www.ccl.net Date: Fri, 19 Jan 1996 10:23:28 -0500 (EST) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 663 Hi, Is there still enyone out there who would like to share room with me at the Sanibel Symposium from 02/28 to 3/2. Please respond to phone numbers below or send an e-mail. With best wishes, Uko -- -- Department of Chemistry | Phones: (352) 392-0554 (office) University of Florida | (352) 392-9865 (room) PO Box 117200 M-B-221 | Fax: (352) 392-9199 Gainesville, | e-mail: uko@ufark2.chem.ufl.edu Florida 32611-7200 | -- -- From bruce@cosy.utmb.edu Fri Jan 19 10:35:16 1996 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.6.10/950822.1) id KAA11585; Fri, 19 Jan 1996 10:34:39 -0500 Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id JAA16274; Fri, 19 Jan 1996 09:40:56 -0600 From: "Bruce A. Luxon" Message-Id: <9601190940.ZM16272@cosy.utmb.edu> Date: Fri, 19 Jan 1996 09:40:49 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SGI PPP for Mac Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Does anyone have some knowledge of SGI PPP setups that allow MacPPP to remotely login over modems? I think I've followed all the directions and can establish a connection but nothing works and it goes dead after about 90 seconds. Thanks in advance! Bruce Luxon -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-chemistry@ccl.net Fri Jan 19 10:41:20 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA11479; Fri, 19 Jan 1996 10:30:02 -0500 Received: from Lilly.com for BAERTSCHI_STEVE_W@Lilly.com by bedrock.ccl.net (8.7.1/950822.1) id KAA00796; Fri, 19 Jan 1996 10:29:59 -0500 (EST) Received: from DECNET-MAIL (RC80281@MCVAX0) by INET.D48.LILLY.COM (PMDF V5.0-4 #10599) id <01I06W7QBMCG0000GW@INET.D48.LILLY.COM> for chemistry@ccl.net; Fri, 19 Jan 1996 10:29:26 -0500 (EST) Date: Fri, 19 Jan 1996 10:29:26 -0500 (EST) From: STEVE BAERTSCHI / 276-1388 / DROP 0724 Subject: Responses to question about UV calculation/CAChe vs Spartan To: chemistry@ccl.net Message-id: <01I06W7QE15E0000GW@Lilly.com> X-VMS-To: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Comp Chem List This is a summary of the four responses I received to my original post regarding the use of the CACHe and Spartan software systems for calculation and prediction of UV spectra. Steve Baertschi Baertschi@Lilly.com ************************* Reply number 1: From: jle@world.std.com Steve, Spartan does not use ZINDO to calculate UV spectra, rather it uses singles and doubles CI in its semi-empirical module. Both are semi-empirical methods - ZINDO will appear as INDO/S in the literature. I think Spartan's pretty easy to use... All of the compute modules have pretty similar interfaces (same style, mostly same contents), and this carries over into the external packages which Spartan supports (such as G9x). Having written a bunch of Spartan, yeah, I'm pretty biased, but the users were pretty/very happy with it. ........... Joe ********************************** Reply number 2: From:mirko@SARA.NL Hi Steve, We are using a CAChe system, although I've never tried to predict UV spectra. What I do know is that it is very easy to use, and that's true for all modules. About the prediction of spectra, you might want to fire the question to the CAChe user group, at cache@pacificu.edu I hope this is of any help! Mirko Mirko Kranenburg Universiteit van Amsterdam J.H. van 't Hoff Research Institute Dept. of Inorganic Chemistry and Homogeneous Catalysis Nieuwe Achtergracht 166 1018 WV Amsterdam The Netherlands tel. +31-20-5256417 fax. +31-20-5256456 e-mail: mirko@sara.nl ************************ Reply number 3: From: reichertd@mirlink.wustl.edu Steve, I can't comment on SPARTAN but I use the CAChe system quite often. I've only calculated spectra a few times and really don't know how it compares to an actual spectra but what I've done seems quite reasonable of course it doesn't take into account solvent effects. You can calculate spectra with ZINDO or in MOPAC with several force fields AM1, PM3,... The CAChe is great for non-experts if you can use a Mac you can use CAChe, personally I find it to become a little cumbersome in that it uses several different modules which load onto its processor card which can lead to noticable delays. As an example I do a MOPAC calculation, so build the molecule in the Editor, minimize in MOPAC so swap out of the Editor and load MOPAC, when finished I want to look at the frontier orbitals so swap out MOPAC load Tabulator and analyze the orbitals, to display the results swap out of Tabulator and load Visulaizer. Cumbersome but easy to use, it also gives very nice graphical output which is easy to understand. It's a simple process to predict reactivity in this manner, you can also predict IR's from MOPAC calculations. Hope this helps, David E. Reichert, Ph.D. Mallinckrodt Inst. of Radiology Div. Radiation Sciences phone: (314)362-8461 fax: (314)362-9940 e-mail: reichertd@mirlink.wustl.edu ************************* Reply number 4: From: echamot@xnet.com Hi Steve, I use the CAChe system quite a bit. I am not as familiar with Spartan. Recently I've been calibrating some ZINDO based UV calculations, so I can comment on your questions about CAChe ZINDO: >Does the CAChe software do a good job of predicting real-world spectra? >Does Spartan have a similar ZINDO module? If it does, how do the two >user-inferfaces compare? CAChe and Spartan both have very good user interfaces for setting up the calculations you want, especially for: >EASE OF USE for a non-expert! CAChe also visualizes the results of a UV calculation nicely, with a simulated spectrum that you can select absorbances from with a mouse click and see the orbitals involved in that transition. CAChe also includes "Project Leader," a molecular spreadsheet that is well suited to developing calibrations (as well as QSPR models), which I think you will want to do. As you may or may not know, ZINDO is the INDO formalism for which parameters (through the first row of transition metals) have been derived specifically to reproduce experimental UV/Visible spectra, by performing a CI (Configuration Interaction) calculation. (It can also predict fluorescence.) So far as the accuracy, it does pretty well in the UV region (within 20 nm or so in my experience), but is less reliable in the Visible region. In different studies, absorption maxima have been found to correlate with the observed lambda max of: unsaturated aldehydes with R^2 0.998, benzenes with R^2 0.94, and a general sampling of organic compounds with R^2 0.925. I have two cautions about calculating absorbances of dyes (in the visible region). The first is that the error is greater, but is somewhat systematic. The thing to do is to do a series of calculations on molecules similar to the one you're interested in to develop a calibration factor and then apply that to your predicted absorbance. Hydrazone dyes, for instance, have a slope of 0.83, whereas anthraquinones have a slope of 2.3. (Masafumi et. al. Dyes and Pigments, 1991, 17, 287-296.) The other caution is that some absorbances are predicted to occur in the visible region, but only with a negligible intensity. Examining the orbitals involved, the intensity is predicted to be near zero because the orbitals are orthogonal. In solution, however, (aside from the effect of solvent shift) the presence of specific solvation molecules must break the symmetry, because those absorbances are, in fact, observed. One last remark on when you get to doing the calculations. You will have the option of several levels of CI to use. In general, after the first several levels, including additional levels of CI only increases the detail of the low end (<200 nm) of the spectrum. In response to your other interests: >I am also interested in these parameters: Reactivity of molecules (where is >the most nucleophilic site, the most electrophilic site, where would radical >attack occur, which hydrogen atom is easiest to abstract, how does the electron >density map look at defined pH's, etc.), pKa estimation, IR prediction, >conformation, etc. Both Spartan and CAChe have very good visualization, not only of orbitals, but also of the surface of the molecule showing the relative susceptibility to nucleophilic, electrophilic, etc. attack. There will be a Midwest CAChe users meeting in January that you may want to attend to get some training and have a chance to see how well you can do what you want with the software. Send email to: manliz@cache.com for more information, or to sign up. I hope that helps. EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 echamot@xnet.com From: BAERTSCHI STEVE W (MCVAX0::RC80281) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") From ferenc@rchsg8.chemie.uni-regensburg.de Fri Jan 19 11:50:14 1996 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.10/950822.1) id LAA12979; Fri, 19 Jan 1996 11:45:26 -0500 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA13475 (5.65c/IDA-1.4.4 for ); Fri, 19 Jan 1996 17:44:41 +0100 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA20657; Fri, 19 Jan 96 17:43:45 +0100 Date: Fri, 19 Jan 96 17:43:45 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9601191643.AA20657@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: CNDO/S-INDO/S-ZINDO/S Dear Cyberchemists: Can anybody out there kindly help me with CNDO/S, INDO/S, or ZINDO/S parameters for Argon and/or other rare gas atoms? Any pointer is wellcome! Thanks a lot! Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- Those who do not archive the past are condemned to retype it! -- Garfinkel & Spafford, Practical Unix Security --------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Jan 19 13:20:15 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA14864; Fri, 19 Jan 1996 13:14:42 -0500 Received: from rs2.hrz.th-darmstadt.de for schulte@ws09.pc.chemie.th-darmstadt.de by bedrock.ccl.net (8.7.1/950822.1) id NAA03069; Fri, 19 Jan 1996 13:14:33 -0500 (EST) Received: from ws09.pc.chemie.th-darmstadt.de (ws09.pc.chemie.th-darmstadt.de [130.83.138.9]) by rs2.hrz.th-darmstadt.de (8.6.12/8.6.12.1ms) with SMTP id TAA89020 for ; Fri, 19 Jan 1996 19:14:24 +0100 Received: by ws09.pc.chemie.th-darmstadt.de (AIX 3.2/UCB 5.64/4.03) id AA12562; Fri, 19 Jan 1996 19:15:20 +0100 From: schulte@ws09.pc.chemie.th-darmstadt.de (Joachim Schulte) Message-Id: <9601191815.AA12562@ws09.pc.chemie.th-darmstadt.de> Subject: Availability of ZINDO To: chemistry@ccl.net Date: Fri, 19 Jan 1996 19:15:18 +0100 (CET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Ladies and Gentlemen, I want to perform some geometry studies of endohedral C82 fullerene complexes. Because the systems are by far too large for a ab initio study I want to use a semiempirical method. Therefore I need a program with good parameters for transition metals like Sc, Y or La, which are not implemented in e.g. MOPAC. ZINDO contains parameters for these elements, so I think it might be useful. Therefore I would like to know, how I could obtain ZINDO or a similar semiempirical program for transition metal compounds. Is it public domain or a commercial program? Who does it offer? Sincerely Yours, Joachim Schulte From owner-chemistry@ccl.net Fri Jan 19 14:20:16 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA16198; Fri, 19 Jan 1996 14:08:38 -0500 Received: from medinah.atc.ucarb.com for jas@medinah.atc.ucarb.com by bedrock.ccl.net (8.7.1/950822.1) id OAA03644; Fri, 19 Jan 1996 14:08:27 -0500 (EST) Received: from smithja.sct.ucarb.com by medinah.atc.ucarb.com (AIX 3.2/UCB 5.64/4.03) id AA28410; Fri, 19 Jan 1996 14:07:02 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 19 Jan 1996 14:09:16 -0400 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Geometric enclosures I'm looking for a program/subroutine/code segment that can generate the defining elements (dimensions) of a specified 3D geometric object (cube, rectangular box, parallelpiped, sphere, ellipsoid, cylinder, cone, etc.) that encloses a molecular structure of given cartesion coordinates using VdW contacts and/or a specified probe radius. The origin and orientation of the geometric shape would correspond to the molecular COM and principle axes. It would be preferable if the program also did the COM/PM analysis. I'd be interested to know if any commercial programs did this, but I need source code (C or FORTRAN) for another program. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH || Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From grechtst@pepvax.pepperdine.edu Fri Jan 19 15:35:17 1996 Received: from pepvax.pepperdine.edu for grechtst@pepvax.pepperdine.edu by www.ccl.net (8.6.10/950822.1) id PAA18069; Fri, 19 Jan 1996 15:29:27 -0500 Received: by pepvax.pepperdine.edu (5.65c/IDA-1.4.4/Pep-5.2) id AA23917 for chemistry@www.ccl.net; Fri, 19 Jan 1996 12:29:10 -0800 From: gregory rechtsteiner Message-Id: <199601192029.AA23917@pepvax.pepperdine.edu> Subject: Dyes To: chemistry@www.ccl.net Date: Fri, 19 Jan 96 12:29:10 PST X-Mailer: ELM [version 2.3 PL11] Hello: I apologize for the trivial nature of this question, but an extensive STN search found nothing. I am looking for the average bond length in the polymethine chain in several cyanine dye series. The compounds are: 3,3'-diethyloxacarbocyanine (di- and tri- carbocyanine as well) iodide and 1,1'-diethylcarbocyanine (di- and tri- crbocyanine as well) iodide A computer calculated value or a resource would be great. Thank you for your time. You effort is appreciated by my professor and by myself. gregory a rechtsteiner -- Pepperdine University Natural Science Division grechtst@pepvax.pepperdine.edu grechtst@pacificnet.net http://pacificnet.net/~grechtst From bruce@cosy.utmb.edu Fri Jan 19 10:34:41 1996 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.6.10/950822.1) id KAA11585; Fri, 19 Jan 1996 10:34:39 -0500 Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id JAA16274; Fri, 19 Jan 1996 09:40:56 -0600 From: "Bruce A. Luxon" Message-Id: <9601190940.ZM16272@cosy.utmb.edu> Date: Fri, 19 Jan 1996 09:40:49 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SGI PPP for Mac Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: R Does anyone have some knowledge of SGI PPP setups that allow MacPPP to remotely login over modems? I think I've followed all the directions and can establish a connection but nothing works and it goes dead after about 90 seconds. Thanks in advance! Bruce Luxon -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-chemistry@ccl.net Thu Jan 18 15:28:55 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA29530; Thu, 18 Jan 1996 15:28:48 -0500 Received: from euch4e.chem.emory.edu for morokuma@euch4e.chem.emory.edu by bedrock.ccl.net (8.7.1/950822.1) id PAA00129; Thu, 18 Jan 1996 15:28:43 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA26738; Thu, 18 Jan 1996 15:28:42 -0500 Message-Id: <9601182028.AA26738@euch4e.chem.emory.edu> Subject: icqc 97 announcement To: molecular-dynamics-news@mailbase.ac.uk Date: Thu, 18 Jan 1996 15:27:20 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Sender: morokuma@euch4e.chem.emory.edu Content-Transfer-Encoding: quoted-printable Status: R FIRST ANNOUNCEMENT THE 9TH INTERNATIONAL CONGRESS OF QUANTUM CHEMISTRY Organized under the auspices of=20 the Internaltional Academy of Quantum Molecular Sciences EMORY CONFERENCE CENTER HOTEL EMORY UNIVERSITY, ATLANTA, GEORGIA, USA JUNE 9-14, 1997 ___________________________________________________________________ ORGANIZING COMMITTEE =20 Ernest R. Davidson Kieji Morokuma (Chair) Henry F. Schaefer, III LOCATION AND DATES =20 Emory Conference Center Hotel, Emory University Atlanta, Georgia USA >From Monday, June 9, 1997 (Gathering) to Saturday, June 14 (Closing Session, Banquet) CORRESPONDENCE =20 Keiji Morokuma 9th ICQC '97 Department of Chemistry Emory University Atlanta, GA 30322 USA Tele: (404) 727-2180 Fax: (404) 727-6586 Email: morokuma@emory.edu PROGRAM =20 The program will include plenary and invited lectures and posters. =20 The conference will be in English. PLENARY SPEAKERS =20 Reinhart Ahlrichs, Institut f=9Fr Physikalische Chemie und Elektrochemie, Karlsruhe, Germany Michele Parrinello, Max-Planck-Institut f=9Fr Festk=9Arperforschung,=20 Stuttgart, Germany Martin Quack, Laboratorium f=9Fr Physikalische Chemie, ETH , Z=9Frich,=20 Switzerland PARTIAL LIST OF INVITED SPEAKERS =20 Alml=9Af Clementi Heller Mayer Apeloig Cremer Hirao Musaev Armentrout Dixon Houk Nascimento Baerends Dunning Iwata Robb Bauschlicher Dykstra Jemmis Scuseria Becke Eisenstein Koch Shaik Bondybey Frenking Koga Stanton Bowers Fu Kozlowski Taylor Carsky Galabov Lischka Urban Cederbaum Gauss Light Yang Ceyer Hall Lorquet Zerner Cioslowski Head-Gordon Makri SESSION TOPICS =20 Methods - Parallel Computation - quantum chemistry code implementation - DFT - Perturbation, Coupled Cluster, etc. (all non-variational methods) - Multi-reference Approaches - Basis Sets and Corrections for Inadequacy - Hybrid Methods (QM/MM, etc.) Applications - Photochemistry - Non-adiabatic Effects - Electronic Structure in Condensed Media - Intermolecular Interactions - Spectroscopy - Chemical Reactivity - Organic Reactions - Homogeneous Catalysts - Solid Surface, Heterogeneous Catalysis - Materials, Solid States - Biological Applications - Dynamics of Nuclear Motion - Statistical Applications - Industrial Applications SATELLITE MEETINGS =20 1. Density-Functional Theory and Computation Dates: June 3-7, 1997 Location: Duke University Durham, North Carolina Contact: Weitao Yang Dept. of Chemistry Duke University Durham, NC 27708-0346 Organizers: Mel Levy and Weitao Yang Email: yang@chem.duke.edu 2. Theoretical Chemistry in Biology: From Molecular Structure=20 to Functional Mechanisms Dates: June 3-7, 1997 Location: Savannah, GA or Charleston, SC Contact: Michael Zerner Quantum Theory Project Univ. of Florida Gainesville, Florida 32611 Organizers: Peter Kollman, Harel Weinstein,=20 and Michael Zerner Email: zerner@qtp.ufl.edu 3. Structural and Mechanistic Organic Chemistry: A Tribute to=20 Professor Norman L. Allinger Dates: June 5-7, 1997 Location: Athens, Georgia Contact: H.F. Schaefer, III Ctr. for Comp. Quan. Chem. Univ. of Georgia Athens, Georgia 30602-2556 Organizers: H.F. Schaefer and P. Schleyer Email: hfsiii@uga.cc.uga.edu 4. Coupled Cluster Theory and Electron Correlation Workshop Dates: June 15-19, 1997 Location: Cedar Key, Florida Contact: Rodney Bartlett Quantum Theory Project University of Florida Gainesville, Florida 32611 Email: bartlett@qtp.ufl.edu=20 5. Interplay between Theory and Experiment in Molecular=20 Spectroscopy and Dynamics Dates: June 15-18, 1997 Location: Memphis, Tennessee Contact: Peter Pulay Dept. of Chem. & Biochem. Univ. of Arkansas Fayetteville, AK 72701 Organizers: Daniel Chapman, Tom Cundari, David Dixon,=20 B. Andes Hess, Bruce Hudson, Henry Kurtz and Peter Pulay Email: pulay@comp.uark.edu __________________________________________________________ Updated information concerning the congress can also be obtained=20 on the internet at http://www.chem.emory.edu/icqc/icqc.html. The second circular containing registration and accommodation=20 information will be mailed in the fall of 1996 to those who=20 return the following response form via fax, mail or email=20 [icqc@euch4g.chem.emory.edu].=20 ___________________________________________________________ Last name First Name Institution Department Address Telephone Fax E-mail ( ) I intend to aprticipate ( ) I intend to present a poster ( ) Please send the second circular From MAILER-DAEMON Thu Jan 18 16:29:21 1996 Received: from ibmmail.COM for by www.ccl.net (8.6.10/950822.1) id QAA00623; Thu, 18 Jan 1996 16:29:16 -0500 Message-Id: <199601182129.QAA00623@www.ccl.net> Received: from ibmmail by ibmmail.COM (IBM VM SMTP V2R3) with BSMTP id 6711; Thu, 18 Jan 96 16:28:19 EST Date: Thu, 18 Jan 1996 16:29:09 EST From: response@ibmmail.com To: chemistry-request@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Subject: Mail Item Format Warning Status: R The mail item that you sent at 21:28:39 GMT on 18 Jan 1996 has been delivered. However, it has been necessary to convert this item into a format that is acceptable to the recipient, DEBAYSPK at IBMMAIL. Information beyond column 79 in the mail item will have been wrapped. From nauss@ucmod2.che.uc.edu Fri Jan 19 09:37:07 1996 Received: from ucmod2.che.uc.edu for nauss@ucmod2.che.uc.edu by www.ccl.net (8.6.10/950822.1) id JAA10304; Fri, 19 Jan 1996 09:37:05 -0500 Received: by ucmod2.che.uc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA29211; Fri, 19 Jan 1996 09:40:03 -0500 From: nauss@ucmod2.che.uc.edu (Jeffrey L. Nauss) Message-Id: <9601190939.ZM29209@ucmod2.che.uc.edu> Date: Fri, 19 Jan 1996 09:39:53 -0500 Reply-To: Jeffrey.Nauss@UC.Edu Organization: Dept. Chemistry, University of Cincinnati X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net, chemistry@www.ccl.net Subject: Seminal and Historical Papers on Molecular Modeling Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: R I'm putting together a collection of seminal and historical papers on molecular modeling and computational chemistry. Specifically, I'm looking for papers that made a major contribution to the field and that helped define molecular modeling. I including in this search just about everything: ab initio, empirical, small molecule, large molecule, MD, MC, QSAR, etc. Some papers I already have are Watson & Crick's paper on DNA structure, Pauling's paper on the alpha helix, Ramachandran's study of allowable phi-psi angles, and the original papers for AMBER and CHARMM. As you can tell, my own bias is to large biomolecules with empirical calculations. I need the most assistance in quantum chemistry and ab initio calculations. So what do you think are the major papers in molecular modeling and computational chemistry? I will produce a summary. Thanks in advance... -- Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * **************************************************************************** From noy@atc.atccu.chula.ac.th Thu Jan 18 03:49:03 1996 Received: from atc.atccu.chula.ac.th for noy@atc.atccu.chula.ac.th by www.ccl.net (8.6.10/950822.1) id DAA19084; Thu, 18 Jan 1996 03:48:51 -0500 Received: by atc.atccu.chula.ac.th (5.57/CFTHAI-2e1.ULTRIX) id AA12979; Thu, 18 Jan 96 15:29:46 GMT From: noy@atc.atccu.chula.ac.th (Teerakiat Kerdcharoen) Message-Id: <9601181529.AA12979@atc.atccu.chula.ac.th> Subject: free energy calculation To: chemistry@www.ccl.net Date: Thu, 18 Jan 1996 15:29:45 +0000 (WET) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 871 Status: RO Dear cyberchemists, I am studying about the molecular dynamics simulation of supramolecules. Could somebody kindly point me out good references of how free energy is calculated by molecular simulations ? I would appreciate any literatures concerning perturbation free energy methods and thermodynamic integration techniques. Thank you very much in advance and have a nice time. take care, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Address: Department of Physics, Mahidol University ,Bangkok 10400 Phone: 5790658, 5793955 ext. 114, mobile 01-4906089 E-mail: noy@atc.atccu.chula.ac.th Homepage: http://www-c724.uibk.ac.at/noy/ Research: Computer Assisted Molecular Design ----------------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Jan 18 03:49:55 1996 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id DAA19096; Thu, 18 Jan 1996 03:49:54 -0500 Date: Thu, 18 Jan 1996 03:49:54 -0500 Message-Id: <199601180849.DAA19096@www.ccl.net> From: Mail Delivery Subsystem for chemistry Subject: Address on reject list To: ccl@www.ccl.net Status: RO ---- Message was rejected (address in reject filee) --- >From noy@atc.atccu.chula.ac.th Thu Jan 18 03:49:51 1996 Received: from atc.atccu.chula.ac.th for noy@atc.atccu.chula.ac.th by www.ccl.net (8.6.10/950822.1) id DAA19084; Thu, 18 Jan 1996 03:48:51 -0500 Received: by atc.atccu.chula.ac.th (5.57/CFTHAI-2e1.ULTRIX) id AA12979; Thu, 18 Jan 96 15:29:46 GMT From: noy@atc.atccu.chula.ac.th (Teerakiat Kerdcharoen) Message-Id: <9601181529.AA12979@atc.atccu.chula.ac.th> Subject: free energy calculation To: chemistry@www.ccl.net Date: Thu, 18 Jan 1996 15:29:45 +0000 (WET) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 871 Dear cyberchemists, I am studying about the molecular dynamics simulation of supramolecules. Could somebody kindly point me out good references of how free energy is calculated by molecular simulations ? I would appreciate any literatures concerning perturbation free energy methods and thermodynamic integration techniques. Thank you very much in advance and have a nice time. take care, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Address: Department of Physics, Mahidol University ,Bangkok 10400 Phone: 5790658, 5793955 ext. 114, mobile 01-4906089 E-mail: noy@atc.atccu.chula.ac.th Homepage: http://www-c724.uibk.ac.at/noy/ Research: Computer Assisted Molecular Design ----------------------------------------------------------------------------- From qojskd@uscmail.usc.es Thu Jan 18 06:22:03 1996 Received: from uscmail.usc.es for qojskd@uscmail.usc.es by www.ccl.net (8.6.10/950822.1) id GAA20306; Thu, 18 Jan 1996 06:21:47 -0500 Received: from [193.144.74.64] (qojskd.usc.es) by uscmail.usc.es (5.67b/1.34) id AA05321; Thu, 18 Jan 1996 12:22:47 +0100 Date: Thu, 18 Jan 1996 12:22:47 +0100 Message-Id: <199601181122.AA05321@uscmail.usc.es> From: "Javier Sardina" To: chemistry@www.ccl.net Subject: Freeware for NMR processing Status: RO Dear netters: It is a pleasure to announce that version 3.1.1 of the NMR processing program SwaN-MR is available, as two compressed-self-expanding files, (via anonymous ftp) from : sfdzuma.usc.es (193.144.75.69) directory /pub/NMR/SwaN-MR.311 This version is a beta release and users are encouraged to test it and submit the bugs they find to the author. SwaN-MR is a FREEWARE program for the Macintosh and PowerMac. It processes and analyzes NMR spectra (1D to 4D, from Varian Gemini, Bruker nad TecMag spectrometers). It is also very useful in annotating, printing and presenting spectra. The program has been written by: Dr. Giuseppe Balacco MENARINI s.r.l. Via Sette Santi, 3 I-50131 Firenze ITALY In order to use SwaN-MR you need to write a SIGNED LETTER (no fax or e-mail messages) to Dr. Balacco requesting a LICENSE. If you want to check out the program before asking for the license you can try Snail-MR (included in the demo file). It does everything that SwaN-MR does but much more slowly. Newest features: - A converter for Nicolet spectra has been added - A module for spectral simulation (up to 9 nuclei) and fitting to experimental data has been added The program's capabilities include: Weighting (9 different window functions) FFT (real, complex, hypercompex, etcI) Phase Correction (1 manual and 2 automatic options) Magnitude representation Baseline Correction (6 options, including 5th degree polynomials and trigonometric series) BasePlane correction Integration (manual and automatic) Least Squares Fitting (to Lorentzian or Gaussian functions) Quanto-mechanical simulations Fast Linear Prediction Digital Solvent Suppression T1 calculation (inversion recovery) Spectral Editing (algebraic addition and much more) Symmetrization I hope that you will enjoy the program. F. Javier Sardina Associate Prof. of Organic Chemistry phone: (34)-81-591085 Departamento de Quimica Organica (34)-81-563100-Ext 4249 Universidad de Santiago de Compostela fax: (34)-81-595012 15706 Santiago de Compostela. SPAIN e-mail: qojskd@usc.es From vince@iris.glvt-cnrs.fr Fri Jan 19 10:27:49 1996 Received: from sivet1 for vince@iris.glvt-cnrs.fr by www.ccl.net (8.6.10/950822.1) id KAA11423; Fri, 19 Jan 1996 10:27:24 -0500 Received: by sivet1.glvt-cnrs.fr (UCX V3.3-7A); Fri, 19 Jan 1996 16:18:05 +0100 Received: by IRIS (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id QAA03477; Fri, 19 Jan 1996 16:33:04 +0100 From: "Vincent NOINVILLE" Message-Id: <9601191633.ZM3475@IRIS> Date: Fri, 19 Jan 1996 16:32:59 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Help: Heme Parameters in AMBER Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: R Hi Netters, I am aware that this question is surely a FAQ. Anyway, as I didn't subscribe to CLL yet and my need for these parameters is great and urgent : Can someone send me (by email) or give some pointers where I can find the AMBER force field parameters for HEMES. I will VERY SOON have to do some calculations on myoglobins and I can't find these hemes parameters. Thanks in advance. Vincent Noinville P.S. Please send any reply to the address in my signature since the reply field is usually corrupted or wrong. Don't use "reply". -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > Vincent NOINVILLE | email : NOINVILLE@GLVT-CNRS.FR < > Lab. de Physicochimie des Biopolymeres | < > 2, Rue Henri Dunant | Tel. : (33 1) 49 78 11 20 < > F-94320 THIAIS, FRANCE | Fax. : (33 1) 49 78 12 08 < *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* From vkitzing@sunny.mpimf-heidelberg.mpg.de Thu Jan 18 04:18:59 1996 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.6.10/950822.1) id EAA19329; Thu, 18 Jan 1996 04:18:57 -0500 Received: from [192.109.43.34] (mac10.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA20536; Thu, 18 Jan 96 10:18:52 +0100 Message-Id: <9601180918.AA20536@otto.mpimf-heidelberg.mpg.de> Date: Thu, 18 Jan 1996 16:13:40 +0000 To: CHEMISTRY@www.ccl.net (Computational Chemistry List) From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Subject: Mobility paradox Status: RO Dear colleges on the Computational Chemistry List, this morning I thought about an apparently simple problem where I do not know a solution jet. Consider a symmetric 1:1 electrolyte system with a single dielectric constant which is divided by a planar surface into a right hand and a left hand side. The cationic and anionic concentrations, cC and cA, on both sides are the same; to obtain global electro neutrality cC == cA is required. Exceptions from this rule are allowed only locally, e.g. within a few Debye length around the boundary. The ionic mobilities are mu1 > mu2 on the right hand side and mu2 and mu1 on the other for cations and anions, respectively. At equilibrium there is no problem. Now an external electric field E is applied and this creates the problem. On the first view one would write the individual ionic fluxes jC and jA far away from the central boundary: left hand side and right hand side cations jC(left) = + F mu1 E cC and jC(right) = + F mu2 E cC anions jA(left) = - F mu2 E cA and jA(right) = - F mu1 E cA where F is Faraday's constant. But this implies jC(left) != jC(right) and jA(left) != jA(right) which violates the particle conservation law. I would assume that such a problem has been discussed in literature. Has anybody some ideas? I will summarize the replies. ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From xiaopeng@astro.ocis.temple.edu Thu Jan 18 10:32:10 1996 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id KAA23488; Thu, 18 Jan 1996 10:32:06 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id KAA00099; Thu, 18 Jan 1996 10:32:00 -0500 (EST) Date: Thu, 18 Jan 1996 10:31:58 -0500 (EST) From: Peking To: ccl Subject: Re: Further question about Gaussian 94 IRC calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Thanks very much for all the response! I found that I may not express myself clearly in the post. I would like to ask you to help me for further information. I add more information in the relative lines below: I first use LST to get a guess structure of the transition state and then use Transition State optimization and frequency to get a first order saddle point. So this structure should be O.K as a starting point for IRC calculation. All this calculation has been saved as ."chk" file by including "%chk=ts" in the input commmand file. Then I use the following input command file to do the IRC --link1-- %chk=ts #T RHF/6-31g(d) IRC=(rcfc, stepsize=5, maxpoint=20) guess=read geom=checkpoint test run tIRC to see if the saddle point connect the starting point to the product 0 1 Could you please give me some more information? > Peking writes: > > > > Dear netters, > > Anybody can kindly point out if it is a bug or I did something wrong? > > > > I used LST and got a saddle point at rhf/6-31g* level, then I try > > to use IRC calculation to confirm that the saddle point connects my > > starting materia and the product. however, when I submitted that job, the > > computer told me that "operation on file out of range" "ER terminatnion > > in NtrErr". "NtrErr called from FileIO" But I did similar job before using > > Gaussian92. > > > > So is this a bug of G94 but not of G92? > > > > Thanks in advance!!! > > > > xiaopeng > > > > This topic is a common source of confusion, which I'd like to > clarify. > > The IRC path leads down from a transition state to the minima it > connects. It starts at a true transition structure, where the forces > are zero and the Hessian has one negative eigenvalue. The algorithm > in Gaussian also expects to start with the Hessian at the TS. > > The LST procedure does NOT locate a transition structure -- it locates > an initial guess for a transition state optimization. In particular, > it finds a point at which the Hessian has at least one negative > eigenvalue (but perhaps more) and at which the forces are far from > zero. The results of an LST calculation are not chemically > meaningful, but are only useful to start an optimization to locate the > actual transition structure. > > In Gaussian 94, LST is really obsolete, since the Opt=QST2 algorithm > both uses synchronous transit methods to locate a guess for the > transition structure and then goes on to complete the optimization. > This replaces the combination of LST and Opt=TS in G92 with a single > (and much more reliable) algorithm. > > The combination of LST and IRC without an intervening Opt=TS in G92 > would give a path, but not one satisfying the definition of the IRC > and not one containing the transition structure, so it's probably > better than G94 won't let you do it. The recommended procedure is > Opt=QST2, Freq, IRC=RCFC. The Freq step both confirms that the > structure found by Opt=QST2 is a proper first order saddle point and > provides the Hessian read by the RCFC option to the IRC. > > Mike Frisch > frisch@lorentzian.com > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: frisch@lorentzian.com > 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 >