From jkshin@radon.sait.samsung.co.kr Thu May 19 00:55:32 1994 Received: from han.hana.nm.kr for jkshin@radon.sait.samsung.co.kr by www.ccl.net (8.6.4/930601.1506) id AAA07842; Thu, 19 May 1994 00:39:16 -0400 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA01993; Thu, 19 May 94 12:35:54 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA03238; Thu, 19 May 94 13:41:37 KST Received: by radon.sait.samsung.co.kr (931110.SGI/920502.SGI) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA27149; Thu, 19 May 94 13:38:25 +0900 Date: Thu, 19 May 94 13:38:25 +0900 From: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9405190438.AA27149@radon.sait.samsung.co.kr> To: chemistry@ccl.net Subject: Atomic charges of halogen containing molecules Dear Netters: Is there anyone who has experiences on calculating atomic charges of halogen(F, Cl ..) containing molecules? I've performed MOPAC6.0/AM1 calculations on those molecules and the results are as follows. | Atomic Charges. C1=O C1 0.302 | O -0.314 HC2-X C2 -0.057 | X, Cl -0.075 I expect that the clorine atom should have some more negative charges. Isn't it(Cl -0.075) too small? Jai jkshin@radon.sait.samsung.co.kr From MAKULA@ARTHUR.CITI2.FR Thu May 19 03:55:34 1994 Received: from ARTHUR.CITI2.FR for MAKULA@ARTHUR.CITI2.FR by www.ccl.net (8.6.4/930601.1506) id DAA15963; Thu, 19 May 1994 03:21:31 -0400 Date: Thu, 19 May 1994 9:20:29 +0200 (WET-DST) From: MAKULA@ARTHUR.CITI2.FR Message-Id: <940519092029.2020a9bc@ARTHUR.CITI2.FR> Subject: Molecular 3D display on Macintosh To: chemistry@ccl.net X-Vmsmail-To: SMTP%"chemistry@ccl.net" Dear netters, does anyone know of a public domain software able to make *nice* displays of 3D molecular structures on a Macintosh, that can be then pasted into word-processing softwares like MS Word ? Remi Le Goas E-mail: remi.le-goas@rp.fr Rhone-Poulenc Agrochimie 14-20 rue Pierre Baizet 69009 Lyon - FRANCE From h.rzepa@ic.ac.uk Thu May 19 04:55:36 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id EAA20401; Thu, 19 May 1994 04:53:38 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <28042-0@punch.ic.ac.uk>; Thu, 19 May 1994 09:52:05 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA18758; Thu, 19 May 94 09:52:25 +0100 Message-Id: <9405190852.AA18758@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 May 1994 09:52:28 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: CCL:Molecular 3D display on Macintosh >Dear netters, > >does anyone know of a public domain software able to make *nice* displays >of 3D molecular structures on a Macintosh, that can be then pasted into >word-processing softwares like MS Word ? CSC Chemistry Viewer V 3.0 (3.1?), a demo version of Chem3D Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From chuck@iaccess.cstat.co.za Thu May 19 08:55:38 1994 Received: from UCTVAX.UCT.AC.ZA for chuck@iaccess.cstat.co.za by www.ccl.net (8.6.4/930601.1506) id IAA01632; Thu, 19 May 1994 08:33:48 -0400 From: Received: from slipper225.cstat.co.za by Uctvax.UCT.AC.ZA (PMDF V4.2-11 #2607) id <01HCIZ377H8G9867D3@Uctvax.UCT.AC.ZA>; Thu, 19 May 1994 14:33:03 +0200 Date: Thu May 19 14:25:39 1994 Subject: Light induced torsional movement To: chemistry@ccl.net Cc: Chuck@psipsy.uct.ac.za Message-id: <01HCIZ380EWI9867D3@Uctvax.UCT.AC.ZA> X-Envelope-to: chemistry@ccl.net MIME-version: 1.0 X-Mailer: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Hi everyone I have a very interesting system in which an apparently torsional movement (by 180 degrees), A-->B, is induced by UV light, and the reverse transformation by heat. I want to eludidate the precise path and mechanism for this by the semi-empirical methods AM1 and PM3. I feel sure that this molecule is leading me into murky waters, and would appreciate your comments. The relevant part of the molecule is shown below : H C=N | \ N ------> N-Ph \ / \ | C=N Ph H / (A) (B) Hyperchem's CIS (with 5 filled and 5 unfilled orbitals) calculation indicated that an excited singlet is produced by UV light, so I optimized this with RHF PM3 (MOPAC 6) from the xtal structure with the keyword EXCITED (i.e. CI with the homo and lumo) Lo, a large torsional movement is indeed produced (about 90 deg), but around the N-N bond (not what I expected). The program stops at a high gradient (about 17 kcal/mol/A) and says the HOF is constant. I'm unable to optimize this any further.. The CI states reported are very close together now (eV): STATE ENERGIES EXPECTATION VALUE OF S**2 S FROM S**2=S(S+1) 1 -3.306163 TRIPLET 2.00000 1.00000 2 -3.218167 SINGLET 0.00000 0.00000 3 -3.202571 SINGLET 0.00000 0.00000 4 0.898535 SINGLET 0.00000 0.00000 (Simple ground state RHF or UHF optimization of this structure returns it to the starting structure A.) ** Should I be optimizing a triplet state from here on ? (This does produce a large torsional movement around C=N, the one I was looking for, but again stops at high gradient) ** What if there is no clear indication of how many frontier orbitals to include in the CI ? ** Is the overall 'plan' to follow the movement sound ? Your help is much appreciated. Charles Marais -- ================================================================= =================================================================== Charles F Marais Phone 27-21-650-2323 or 788-2248 Southern Scientific Fax 27-21-788-6613 17 Capri Rd E-mail Chuck@psipsy.uct.ac.za St James Chuck@iaccess.cstat.co.za South Africa 7945 =================================================================== From ccl@probe.ac1.uni-duesseldorf.de Thu May 19 09:57:00 1994 Received: from probe.ac1.uni-duesseldorf.de for ccl@probe.ac1.uni-duesseldorf.de by www.ccl.net (8.6.4/930601.1506) id JAA03177; Thu, 19 May 1994 09:01:24 -0400 Received: by probe.ac1.uni-duesseldorf.de (5.61/1.34) id AA20645; Thu, 19 May 94 14:58:56 +0200 From: ccl@probe.ac1.uni-duesseldorf.de (Computational Chemistry List) Message-Id: <9405191258.AA20645@probe.ac1.uni-duesseldorf.de> Subject: AM1-PM3 To: chemistry@ccl.net (Theochem-Liste) Date: Thu, 19 May 1994 13:58:56 +0100 (MET) X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 391 Hi, folks! We are using AM1 and PM3 and would like to know if there are any differences between the two concerning the theoretical basis. Are the Hamiltonians used different or does the only difference lie in the parametrisation procedure? We already know that the core-core repulsion terms vary slightly between the two methods. Looking forward to get some information! Bye Kay & Ruth From ADAMO@CHEMNA.DICHI.UNINA.IT Thu May 19 10:55:39 1994 Received: from CHEMNA.DICHI.UNINA.IT for ADAMO@CHEMNA.DICHI.UNINA.IT by www.ccl.net (8.6.4/930601.1506) id KAA09394; Thu, 19 May 1994 10:41:34 -0400 From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V4.2-11 #3559) id <01HCJ3KF0K2O00036O@CHEMNA.DICHI.UNINA.IT>; Thu, 19 May 1994 16:42:04 CET Date: Thu, 19 May 1994 16:42:04 +0100 (CET) Subject: Schaefer, Horn and Ahlrichs basis sets To: chemistry@ccl.net Message-id: <01HCJ3KF1D0200036O@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: ADAMO MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCl friends, several days ago I posted a question on the basis sets of Schaefer, Horn and Ahlrichs (JCP 97 (1992) 2571). I received several messages, which can be summarized as follows: the basis are at this internet address 129.13.107.186 login anonymous pass e-mail address the basis sets are in /pub/basis directory. Thanks to all Carlo From MMADRID@B.PSC.EDU Thu May 19 10:57:53 1994 Received: from B.PSC.EDU for MMADRID@B.PSC.EDU by www.ccl.net (8.6.4/930601.1506) id KAA09161; Thu, 19 May 1994 10:37:45 -0400 From: Date: Thu, 19 May 1994 10:38:40 -0400 (EDT) To: chemistry@ccl.net Message-Id: <940519103840.24c25828@B.PSC.EDU> Subject: CCL: Computational X-Ray worskshop offered at PSC COMPUTATIONAL X-RAY CRYSTALLOGRAPHY WORKSHOP Pittsburgh Supercomputing Center July 24-27, 1994 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a computational X-ray crystallography workshop. The objective of this workshop is to introduce participants to the theoretical and computational analysis of X-ray crystallography data of both small molecules and macromolecules. Topics will include: the theoretical basis for the minimal function, simulated annealing, molecular replacement, phasing and density modification. The programs SnB, based on Shake and Bake, and X-PLOR will be extensively discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided during the hands-on sessions, or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. Axel Brunger, Yale University, Dr. Herbert Hauptman, Medical Foundation of Buffalo, Inc. and Dr. Russ Miller, State University of New York at Buffalo. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for academic participants are supported by this grant. Enrollment is limited to 20. Deadline for applications is: May 24, 1994. PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE COMPUTATIONAL X-RAY CRYSTALLOGRAPHY July 24-27, 1994 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by MAY 24, 1994 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, 412/268-4960, or send electronic mail to blankens@psc.edu (internet) *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From jsb2@camsci.com Thu May 19 11:55:41 1994 Received: from camsci.com for jsb2@camsci.com by www.ccl.net (8.6.4/930601.1506) id LAA11274; Thu, 19 May 1994 11:09:25 -0400 From: Date: Thu, 19 May 94 11:10:37 EDT Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA00309; Thu, 19 May 94 11:10:37 EDT Message-Id: <9405191510.AA00309@camsci.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:Molecular 3D display on Macintosh >>does anyone know of a public domain software able to make *nice* displays >>of 3D molecular structures on a Macintosh, that can be then pasted into >>word-processing softwares like MS Word ? >CSC Chemistry Viewer V 3.0 (3.1?), a demo version of Chem3D Actually, while the CSC Chemistry Viewer will produce nice displays, it will NOT allow them to be pasted into MS Word. Copy-and-paste is specifically disabled in the demo, but it is, of course, fully functional in the commercial version of CSC Chem3D. Also the Chemistry Viewer is NOT in the public domain. It may be freely distributed, but it is still copyrighted. Jonathan Brecher International Marketing Manager Cambridge Scientific Computing, Inc. jsb@camsci.com From scsupham@reading.ac.uk Thu May 19 12:55:42 1994 Received: from mail2.rdg.ac.uk for scsupham@reading.ac.uk by www.ccl.net (8.6.4/930601.1506) id MAA17604; Thu, 19 May 1994 12:52:41 -0400 Received: from reading.ac.uk by mail2.reading.ac.uk with SMTP - Local (PP) id <15525-0@mail2.reading.ac.uk>; Thu, 19 May 1994 17:42:54 +0100 Date: Thu, 19 May 1994 17:38:28 +0100 (BST) From: John Upham Subject: DFT convergence with TM cluster systems To: chemistry@ccl.net Cc: scsupham@reading.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 517 Dear All, Is there a known problem with DFT convergence when dealing with systems of transition metal clusters ? I would appreciate details of any example clusters which converge well. I'm using DMol v2.35 for this work if that is relevant. john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@reading (JANET), john@chemistry.reading Voice: +44 734 875123 x7441 (day), Fax: +44 734 311601 From WANG@IRBM.IT Thu May 19 13:51:34 1994 Received: from V1.IRBM.IT for WANG@IRBM.IT by www.ccl.net (8.6.4/930601.1506) id NAA20982; Thu, 19 May 1994 13:51:30 -0400 From: Date: Thu, 19 May 1994 19:54:26 +0200 (WET-DST) To: chemistry@ccl.net Message-Id: <940519195426.1875@IRBM.IT> Subject: RE: CCL:Atomic charges of halogen containing molecules (Regarding to the question from Jaikwang Shin) Jai, You are right. The MEP fitted atomic charges of halogen atoms should be relatively small. The reason is that the electrostatic potentials around these atoms are much less negative than those of Oxygen and Nitrogen atoms in molecules. Examples may be found in J.Comp.Chem.14(1993)1101 for your interest. The charges, which might be too small in your calculation, are those of the atoms in the carbonyl group. Below is a test I did on SGI with the method in the paper mentioned above (also see JCC 15(1994)200). The MEP charge of the chloride is small in my calculation, too. The method has been coded and become available in MOPAC93. > AM1 1SCF QPMEP CONNOLLY > CH3COCH2CL, H=-55.036128 KCAL(am1,gas) > > (......) > NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS > > ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY > 1 O -0.2716 6.2716 > 2 C 0.2234 3.7766 > 3 C -0.2697 4.2697 > 4 C -0.1836 4.1836 > 5 H 0.1112 0.8888 > 6 H 0.1177 0.8823 > 7 H 0.1026 0.8974 > 8 H 0.1340 0.8660 > 9 H 0.1230 0.8770 > 10 Cl -0.0869 7.0869 > DIPOLE X Y Z TOTAL > POINT-CHG. 1.613 0.461 -1.036 1.972 > HYBRID 0.317 -0.078 -0.036 0.329 > SUM 1.930 0.383 -1.072 2.241 > > (......) > > ATOMIC CHARGES DERIVED FROM MOLECULAR ELECTROSTATIC POTENTIAL > (CONNOLLY SURFACES) > > ATOM NO. TYPE CHARGE > 1 O -0.4291 > 2 C 0.5904 > 3 C1 -0.3703 > 4 C2 -0.4495 > 5 H(C1) 0.1203 > 6 H(C1) 0.1152 > 7 H(C1) 0.1089 > 8 H 0.1975 > 9 H 0.1782 > 10 CL -0.0615 > > NUMBER OF POINTS 695 > RMS DEVIATION 1.1522 > RRMS DEVIATION 0.1400 > > > DIPOLE MOMENT EVALUATED FROM THE MEP CHARGES > D(X) D(Y) D(Z) TOTAL > 1.8287 0.4348 -1.1277 2.1920 > > TIME TO CALCULATE MEP 0.36 SECONDS > Ciao, Bingze ======================================================== Bingze Wang, Ph.D. IRBM Via Pontina Km 30,600 00040 Pomezia (Roma) Italy Tel +39-6-91093635 fax +39-6-91093225