From jkl@ccl.net Sun Apr 24 00:31:01 1994 Received: from hawkeye.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id XAA23870; Sat, 23 Apr 1994 23:42:39 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by hawkeye.ccl.net (8.6.4/920428.1525) id XAA23726; Sat, 23 Apr 1994 23:42:40 -0400 Date: Sat, 23 Apr 1994 23:42:40 -0400 Message-Id: <199404240342.XAA23726@hawkeye.ccl.net> To: chemistry@ccl.net Subject: List of conferences available via gopher Cc: jkl@ccl.net Dear Netters, I changed the format of the file which holds conferences which may be of interest for this forum. The file has now a maibox format, so it can be scanned easily by your "mail" program (each conference description will look like a separate e-mail message with the subject giving the starting date and conference name). You can get it via anonymous ftp: www.ccl.net:/pub/chemistry/info/conferences But first of all you can view it via gopher as a mailbox. So add this to your bookmarks in .gopherrc # Type=1 Name=conferences Path=m/info/conferences Host=www.ccl.net Port=73 or you can go there the hard way: gopher www.ccl.net 73 info conferences We also started WWW page for the list: http://ccl.net/chemistry.html It is under construction, so it will change daily for some time, but will get more stable at some point. Jan Labanowski jkl@ccl.net From mei@atlas.rc.m-kasei.co.jp Sun Apr 24 04:31:06 1994 Received: from relay2.UU.NET for mei@atlas.rc.m-kasei.co.jp by www.ccl.net (8.6.4/930601.1506) id EAA25165; Sun, 24 Apr 1994 04:08:23 -0400 Received: from uucp4.uu.net by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwmzg29938; Sun, 24 Apr 94 04:08:22 -0400 Received: from kddlab.UUCP by uucp4.uu.net with UUCP/RMAIL ; Sun, 24 Apr 1994 04:08:23 -0400 Received: from kddfuji by kddlab.kddlabs.co.jp (5.61/6.2Junet) id AA13546; Sun, 24 Apr 94 16:59:56 +0900 Received: from kogwy.cc.keio.ac.jp by kddfuji.kddlabs.co.jp (5.67+1.6W/KDD-1.02MX) id AA21334; Sun, 24 Apr 94 16:59:20 JST Received: by kogwy.cc.keio.ac.jp (5.67+1.6W+comp-patch/2.8Wb) id AA08907; Sun, 24 Apr 94 16:59:17 JST Received: from atlas.rc.m-kasei.co.jp by mkcgwy.rc.m-kasei.co.jp (4.1/6.4J.6) id AA16807; Sun, 24 Apr 94 16:26:52 JST Received: by atlas.rc.m-kasei.co.jp (4.1/6.4J.6) id AA09743; Sun, 24 Apr 94 16:26:52 JST From: mei@atlas.rc.m-kasei.co.jp (Akinori MURAKAMI) Message-Id: <9404240726.AA09743@atlas.rc.m-kasei.co.jp> To: chemistry@ccl.net (Computational Chemistry) Cc: h8714031@hkuxa.hku.hk (Mok Kam Wah), mei@atlas.rc.m-kasei.co.jp Subject: Re(About symmetry and electronic occupancy) Date: Sun, 24 Apr 94 16:26:52 +0900 KWK writes Suppose for a diatomic molecules with three unpair electrons in s,p and d (s=sigma, p=pi, d=delta ) molecular orbital with two electron up-spin and one down-spin. The 2-PI and 2-DELTA states can arise from these electron occunpancy, if I know which orbital the down-spin electron in, can I tell whether it is a 2-PI or 2-DELTA state. For example s p d (orbitals) (u: up-spin, d:down-spin) u u d => 2-PI? d u u => 2-DELTA? What is the electronic configuration for 2-PI for such case? Your question luck information. And we can not describe three open shell state by one slater determinant except high spin state. Althogh sz of up, up, down is 1/2 but it is not correct s**2 function. Doublet spin functions are (1/sqrt(2))(|uud|-|udu|) (1/sqrt(6))(|uud|+|udu|-2|duu|) An also the orbitals are doubly degenerate except sigma orbital in linear molecule. For electronic configuration, we specify sigma*1, pi*1, delta*1, For configuration state function, we have to specify pi+,pi-,delta+,delta- ................................... !!! Note !!! Akinori MURAKAMI My user-ID is not murakami Mitsubishi Kasei Corporation There are more than two murakami Computational Science Laboratory Research Center, Yokohama, JAPAN e-mail mei@m-kasei.co.jp ................................... From inoue@greencross.co.jp Sun Apr 24 08:31:08 1994 Received: from uucp0.iij.ad.jp for inoue@greencross.co.jp by www.ccl.net (8.6.4/930601.1506) id IAA25927; Sun, 24 Apr 1994 08:00:02 -0400 Received: from wincgw1.winc.ad.jp (wincgw1.winc.ad.jp [202.15.200.1]) by uucp0.iij.ad.jp (8.6.8+2.4Wb/3.3Wb-UUCP) with SMTP id UAA17437 for ; Sun, 24 Apr 1994 20:59:59 +0900 Received: by wincgw1.winc.ad.jp (5.67+1.6W/4.18:3.7:winc:931216) id AA17456; Sun, 24 Apr 94 21:00:17 JST Received: by gccss2.greencross.co.jp (4.1/6.4J.6-agu4) id AA22112; Sun, 24 Apr 94 20:44:57 JST Date: Sun, 24 Apr 94 20:44:57 JST From: inoue@greencross.co.jp (Yoshihisa Inoue) Message-Id: <9404241144.AA22112@gccss2.greencross.co.jp> To: chemistry@ccl.net Subject: Re: Quant. Chem. Lit. Database (QCLDB) Dr.J.Martin asked >pardon me for asking, but can someone provide me with some information >regarding the quantum chemistry literature database that is based in >Japan. Quantum Chemistry Literature Database(QCLDB) contains 23239 (@_@) literatures now, and last year about 2000 literatures was updated. It collected ab initio calculation bibliography from 1978. The literature citations contained in QCLDB are restricted to those concerning ab initio computations of atomic and molecular electronic structures. A reference concerned only with the theory without reporting any computation results is included, however, if it is judged to have some relevance to molecular ab initio calculations. No semiempirical calculations are cited.(^_^;) The keywords are Author(s), Journal name , Volume, Page, Year, Compound formulas, Methods of calculation, BASIS SETS, Physical properties, Comments, and ID number. Output example was already shown just a year ago, >From: siroiss@cerca.umontreal.ca (Suzane Sirois) >Subject: CYSTEINE GEOM >Date: Sun, 4 Apr 1993 00:47:41 -0500 (EST) > >THEODJ=Theochem (J.Mol.Struct.) >U SCHAFER L,SIAM K,KLIMKOWSKI V J,EWBANK J D,VAN ALSENOY C > JO THEODJ > VO 63 > PA 361 > YE 90 > CO C3H7NO2S > ME RHF > BA GDZ,GEXT > PR GEOM > COM CYSTEINE , GEOMETRIES OF 10 CONFORMATIONS , 3-321G , POTEN > TIAL-ENERGY CURVES FOR THE N-C-C=O AND H-C-C-S TORSIONS , T > HE DEPENDANCE OF BOND ANGLES ON TORSIONAL ANGLES > ID 18381 It runs on IBM3090(VM/SP),Hitac M-series(VOS3),Hitac S-820(HAP Fortran), FACOM M-series(OSIV),VAX-11/780(VMS),CRAY2(UNICOS4.0),IRIS-4D(Irix System V), SUN Sparc(4.1), HP(HP-UX5.0),HP/APOLLO DN1000(DOMAIN/OS, FTN10.7), ALLIANT(CONVENTRIX/FX/FORTRAN 4.2), HItachi 2050G(HI-UX), IBM-RS6000. It needs about 20-40 Mbytes disk. The media for distribution is Magnet tape(non-label/ASCII 6250 or 1600) or Magnet tape (non-label/EBCDIC 6250 or 1600) or 1/4" Cartridge tape(150MB UNIX/tar(QIC120)). Because It is released every October, the licence fee is higher between October to March, and cheaper between April to September. October to March: Academic about 60000yen (almost $ 600) Industr. about 210000yen (almost $2000) April to Septem.: Academic about 50000yen (almost $ 500) Industr. about 160000yen (almost $1500) If you want more information, please contact to Ms.Kowata. Japan Association for International Chemical Information 6-25-4 Hon-Komagome, Bunkyo-ku, Tokyo 113 Japan tel: +81-3-5978-3622 fax: +81-3-5978-3600 telex: 272-3805 (JAICI J) ___/ ___/ ___/ Yoshihisa INOUE (^_^) / / / the Green Cross Corp. / _ / / / 2-25-1 Shodai-Ohtani,Hirakata,Osaka 573 JAPAN / / / / tel: +81-720-56-9328 _____/ ____/ ____/ fax: +81-720-57-5020 From matt@mercury.aichem.arizona.edu Sun Apr 24 18:31:12 1994 Received: from mercury.aichem.arizona.edu for matt@mercury.aichem.arizona.edu by www.ccl.net (8.6.4/930601.1506) id SAA07041; Sun, 24 Apr 1994 18:01:54 -0400 Received: by mercury.aichem.arizona.edu (5.57/Ultrix3.0-C) id AA03390; Sun, 24 Apr 94 14:51:10 -0700 Date: Sun, 24 Apr 1994 14:48:31 -0700 (MST) From: Matthew Stahl Subject: MM comparison of diasteriomers (summary) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings Netters, Here are the two replies to the question: Can the strain energies of diasteriomers (sterioisomers that are not mirror images) be compared with any validity? Thanks again for all the responses. ---------------------------------------------------------- From rs0thp@RohmHaas.Com Sun Apr 24 14:46:13 1994 Date: Wed, 20 Apr 1994 16:23:27 +22305458 (EDT) From: "Dr. Tom Pierce" To: Matthew Stahl Subject: Re: CCL:MM calc'n of stereoisomers Assuming that you are still asking the question.. Sure - The comparisons will be as accurate as the forcefield . Note that in a multiple-minima problem you have to check your minimia. (Step 1 finding an energy for a isomer - this needs to be checked to see if the minimizer is locked in a local minimum, ie use different starting points.. step 2 - invert the chiral center and minimize.. Note that you also will need somewhat different starting points after the inversion, since your minimizer will likely get stuck in some local minimum. The reason that you might need to try different starting points is that usually a minimizer will at the beginning of a minimization, chose a large step change for minimizing the energy. This step change is very dependent on the initial derivatives and can push a molecule into a different local minimum. Step Three - Is there a difference? Is it within the error of the forcefield? If it is within the error of the forcefield then there is no practical difference.. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." --------------------------------------------------------------- From doherty@msc.edu Sun Apr 24 14:46:26 1994 Date: Wed, 20 Apr 1994 16:24:14 -0600 From: "David C. Doherty" To: Matthew Stahl Subject: Re: CCL:MM calc'n of stereoisomers >What I was >concerned with is the comparison of diasteriomers with mechanics. Can the >strain energies of diasteriomers (sterioisomers that are not mirror images) >be compared with any validity? Most certainly. For instance, there have been many successful studies using MM to look at relative enrgetics of syndiotactic vs. isotactic polymers. For instance, @article{Doherty_and_Hopfinger_(1989), author = "David C. Doherty and Anton J. Hopfinger", title = "Molecular Modeling of Polymers. 6. Intramolecular Conformational Analyses and Molecular Dynamics of Syndiotactic Polystyrene", journal = "Macromolecules", year = "1989", volume = "22", pages = "2472" looks at the energetics of syndiotactic polystyrene, but also contains references to its diastereomer, isotactic polystyrene. --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From keiko@si.fi.ameslab.gov Sun Apr 24 19:31:13 1994 Received: from mailhub.iastate.edu for keiko@si.fi.ameslab.gov by www.ccl.net (8.6.4/930601.1506) id TAA07439; Sun, 24 Apr 1994 19:10:53 -0400 Received: from si.fi.ameslab.gov by mailhub.iastate.edu id AA02974; Sun, 24 Apr 1994 18:11:25 -0500 Received: by si.fi.ameslab.gov (AIX 3.2/UCB 5.64/4.03) id AA49783; Sun, 24 Apr 1994 18:11:10 -0500 From: keiko@si.fi.ameslab.gov (Keiko Takano) Message-Id: <9404242311.AA49783@si.fi.ameslab.gov> Subject: QCLDB To: chemistry%ccl.net@iastate.edu (CCL) Date: Sun, 24 Apr 94 18:11:10 CDT Cc: keiko@si.fi.ameslab.gov (Keiko Takano) X-Mailer: ELM [version 2.4beta PL7] Content-Type: text Content-Length: 1240 Dr. J. Martin asked about QCLDB. We, the QCDB (Quantum Chemistry DataBase) group, have been organizing QCLDB (Quantum Chemisry Literature Data Base). It has been developing by many quantum chemists, who voluntarily participated in this project as abstractors and reviewers, who are working not only in Japan but also in other countries. An introduction by Dr. Yoshihisa Inoue was perfect for the on-line version of QCLDB. We greatly appreciate his nice introduction. The retrieval system is much better, if you have any computer facilities in your site. We also have been publishing a supplement each year covering publications of the preceding year as a special issue of THEOCHEM. It is published every December. You can get a copy of it by Elsevier. JAICI(Japan Association for International Chemical Information) is responsible for the distribution of the on-line system of QCLDB. (Ms. Kowata, FAX:+81-3-5978-3600) The office of the QCDB group is located at Ochanomizu University.(Prof. Haruo Hosoya, FAX:+81-3-3942-2815) Keiko Takano, PhD. e-mail: keiko@si.fi.ameslab.gov Department of Chemisry Fax: +81-3-3942-2815 Ochanomizu University Voice: +81-3-3943-6326 Bunkyo-ku, Tokyo 112 JAPAN From marty@ionchannel.med.harvard.edu Sun Apr 24 20:31:14 1994 Received: from harvard.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.4/930601.1506) id TAA07574; Sun, 24 Apr 1994 19:40:04 -0400 Received: by harvard.harvard.edu (5.54/a0.25) (for CHEMISTRY@ccl.net) id AA10928; Sun, 24 Apr 94 19:40:16 EDT Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA13661; Sun, 24 Apr 94 19:36:21 EDT Received: from [134.174.159.129] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:CHEMISTRY@ccl.net id AA17020; Sun, 24 Apr 94 19:39:41 -0700 Message-Id: <9404250239.AA17020@ionchannel.med.harvard.edu> X-Sender: marty@ionchannel.med.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 24 Apr 1994 18:39:54 -0400 To: rcenter@biosym.com From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: Can Insight run strictly in X? Cc: CHEMISTRY@ccl.net X-Mailer: Recently, people were asking about X-windows emulators on PC's. >Hello: > You need a Xserver to do this, try to find on the net a demo >called Xappeal for DOS. If you're running MS-Windows you can try another >demo, Xwin. > >Pedro I am running Xwin and am very happy with it. Here, we use both Tripos' Sybyl as well as biosym's Insight on SGI indigos. Sybyl runs fine with Xwin. Apparently, it can detect that the terminal is strictly an X-windows emulator and then adjusts the display parameters appropriately. Insight must use a mixture of X / GL graphics as the default and this blows up when you try to access it with Xwin beacuse it cannot handle GL. Does anyone know how to get insight to run with strictly in X so it can be run on X terminals such as Xwin? Thanks, Marty (I'll summarize & post if there's interest) ========================================================================= Martin J. Gallagher phone: (617) 432-1720 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 =========================================================================== From javito@netcom.com Sun Apr 24 21:31:15 1994 Received: from netcom9.netcom.com for javito@netcom.com by www.ccl.net (8.6.4/930601.1506) id UAA08072; Sun, 24 Apr 1994 20:32:28 -0400 Received: from localhost by netcom9.netcom.com (8.6.4/SMI-4.1/Netcom) id RAA28609; Sun, 24 Apr 1994 17:33:38 -0700 From: javito@netcom.com (James Vito) Message-Id: <199404250033.RAA28609@netcom9.netcom.com> Subject: jmr.zip ftp address change To: chemistry@ccl.net Date: Sun, 24 Apr 1994 17:33:38 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 266 jmr.zip can now be found at ftp.wustl.edu /pub/msdos_uploads/chemistry This is a molecule renderer for DOS. The program is a ray tracer that yields 24-bit true color targa images of molecules. atomic coordinate input file supplied by the user. javito@netcom.com