From owner-chemistry@ccl.net Thu Jan 25 04:52:01 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA23801; Thu, 25 Jan 1996 04:44:17 -0500 Received: from ausone.lpct.u-bordeaux.fr for pesquer@lpct.u-bordeaux.fr by bedrock.ccl.net (8.7.1/950822.1) id EAA09804; Thu, 25 Jan 1996 04:44:11 -0500 (EST) From: Message-Id: <199601250944.EAA09804@bedrock.ccl.net> Received: from mac4.lpct.u-bordeaux.fr by ausone.lpct.u-bordeaux.fr with SMTP (1.38.193.4/16.2) id AA29841; Thu, 25 Jan 1996 10:41:43 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: Eudora F1.4.2 Date: Thu, 25 Jan 1996 10:56:46 +0000 To: chemistry@ccl.net Subject: 5 CONGRES DES CHIMISTES THEORICIENS FRANCAIS @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 5eme Reunion des Chimistes Theoriciens Francais @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 5eme R C T F 21 - 25 Octobre 1996 - Arcachon sous l'egide de l'Universite Bordeaux I de la Region Aquitaine du Ministere de l'Education Nationale et du Centre National de la Recherche Scientifique Objectif et Programme Les reunions des Chimistes Theoriciens Francais, qui s'etaient tenues a Orsay (1983), au col de la Schlucht (1985), a Bombannes (1987) et a Chantilly (1989), avaient permis de faire le point sur l'avancement de la discipline et de constater son impact grandissant dans le monde des experimentateurs. Cette 5eme Reunion des Chimistes Theoriciens Francais a pour but de renouer les liens entre les membres de la communaute, de faciliter les contacts entre les generations et d'etablir un bilan ainsi qu'une prospective sur les avancees de la Chimie Theorique. Cette reunion doit etre largement ouverte a tous les axes de la Chimie Theorique actuelle. Neanmoins, dans un souci d'harmonie des presentations, nous proposons de consacrer les quatre matinees aux quatre themes larges suivants: - Les methodes de la Chimie Quantique - Le langage orbitalaire en Chimie Theorique - La reactivite et la dynamique reactionnelle - Les systemes complexes: vers le macroscopique Un certain nombre de collegues chercheurs confirmes sont deja pressentis pour les conferences du matin (J. Angyan, M. Benard, X. Chapuisat, M. Field, J. Hafner, J. L. Heuilly, Y. Jean, C. Leforestier, C. Marsden, G. Pastor, P. Rosmus, A. Savin). Les communications de l'apres-midi seront reservees en priorite aux jeunes chercheurs theoriciens recrutes recemment dans nos laboratoires. Cette Reunion se tiendra au Palais des Congres d'Arcachon du 21 au 25 octobre 1996. Organisation des Journees -3 conferences d'une heure au maximum chacune discussions incluses (4 conferences le vendredi), chaque matin (4 matinees, soit 13 conferences), - 5 a 6 communications orales de 20 minutes chacune, en fin d'apres-midi (3 apres-midis, soit de 15 a 18 communications) - 2 seances de posters le mardi et le mercredi, en soiree. Comite Scientifique J. P. Daudey (Toulouse), C. Leforestier (Montpellier), J. C. Rayez (Bordeaux), J. L. Rivail (Nancy), F. Volatron (Orsay). Comite d'Organisation J.C. Rayez (responsable), F. Achard (tresorier), L. Bonnet, L. Ducasse, A. Fritsch, Ph. Halvick, M. Kressler, D. Liotard, M. Pesquer, M.-T. Rayez,, A. Salin, T. Stoeklin, G. Volpilhac Inscription $$$$$$$$$$$$ Le montant des frais d'inscription est de 900F. Logement et repas Le montant total des frais d'hebergement est de 2100F. Le logement sera assure dans des hotels de categorie 2* directement situes a proximite immediate du palais des Congres. Les repas seront servis sur le lieu du congres. Ce montant sera a regler directement au Palais des Congres lors de l'inscription definitive (la date limite pour cette inscription sera indiquee dans la 2eme circulaire). Renseignements et correspondance $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ 5eme RCTF Laboratoire de Physico-Chimie Theorique URA 503 CNRS Universite Bordeaux I, 33405 Talence Cedex. Tel. : 56.84.63.13 / FAX : 56.84.66.45 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ e.mail : achard @ lpct.u-bordeaux.fr <--- <--- <----<--------<------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Bulletin d'inscription( a retourner par le reseau svp) a retourner avant le 15 mars 1996 Nom : Mr / Mme / Mlle ........................................................................ Prenom : ............................................................... Organisme : ........................................................................ ........................................................................ ........................................................................ Adresse : ........................................................................ ........................................................................ Tel. : FAX : e-mail : je souhaite participer et recevoir la 2eme circulaire: ................. je souhaite presenter : un poster ........................................ une communication orale........................... Titre : ................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ **************************************************** * * Michel PESQUER E-Mail: pesquer@lpct.u-bordeaux.fr * **************************************************** * Labo: Physicochimie theorique. - U.B.I. - 33405 Talence Cedex * * Tel 56 84 63 12 Fax 56 84 66 45 **************************************************** * Delegation Regionale du CNRS. - B.P.105 - 33402 Talence Cedex * * Tel 56 37 80 80 Fax 57 96 10 56 * *************************************************** From thomas_w@btm2x2.mat.uni-bayreuth.de Thu Jan 25 08:22:03 1996 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.6.10/950822.1) id IAA25291; Thu, 25 Jan 1996 08:18:43 -0500 Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA29984; Thu, 25 Jan 96 14:18:10 +0100 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA25708; Thu, 25 Jan 96 14:14:37 +0100 Date: Thu, 25 Jan 96 14:14:37 +0100 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9601251314.AA25708@btm2x2.mat.uni-bayreuth.de> To: chemistry@www.ccl.net, thomas_w@www.ccl.net Subject: Summary: Simulations in Combinatorial Chemistry Dear Netters, last week I posted the following question to this list: >I try to learn more about Combinatorial Chemistry. I have checked >the NetSci issue last summer and some review articles like the ones >by Gallop, Gordon, Barrat et al. (J. Med. Chem. 37). Most papers >only tell how a combinatorial library is built experimentally. Since I have no >laboratory, but just a computer, I want to do this as a simulation, >i.e. generate the diversity in a file and apply a similarity >search (or any other) method for screening. >Last spring there was a paper by T. Carell, J. Rebek et al. in >Chemistry & Biology, which was quite detailed. Unfortunately >I couldn't find any other. I got 6 inquiries and 5 answers to it, but in general I have the feeling that there are more people out there who want to know than those who do know. If in the future anybody else comes across with some interesting material, I will certainly be glad to hear about it, too. Since some asked, the source of the paper cited above is: "New promise in combinatorial chemistry: synthesis, characterization, and screening of small-molecule libraries in solution" T. Carell, E.A. Wintner, A.J. Sutherland, J. Rebek jr., Y.M. Dunayevskiy, P.Vouros Chemistry & Biology, 1995, Vol. 2, No 3, p. 171-183 The other answers are as follows: ---------------------------------------------------------------------- From: dpoppi@CHBS.CIBA.COM (Dieter Poppinger) There is a good paper by E.Martin in J.Medicinal Chemistry 38 (1995) p. 1431. Also there is something by Keith Davies in NetSci last year. Most other stuff is just talked about at conferences. ---------------------------------------------------------------------- From: Arthur Wang I am a Ph.D student majoring in computer-aided drug design. I have developed a computer program to generate ligands which can fit to the target receptor. The method to construct molecular models is so-called "atom-growing". That is, I let different types of atoms to be grown from a seed fragment. And the most of important, I take account all possible combinations of atom patterns. So I can finally get a library for a specific receptor. Then a following program is used to evaluate the quality of binding of each molecule. To some extent, it is the simulation of combinatorial chemistry on computer. You can look at my homepage. There is a brief abstract of my paper. The paper have been submitted to J.Chem.Inf.Comp.Sci for consideration. For more details, just contact with me. ----------------------------------------------------------------------- From: "Alberto Gobbi" J. Chem. Inf. Comput. Sci 1995, 35, 1026 may be interesting for you. It decribes some aspects which are realized in the Comb. Chem. software of Daylight Inc. (www.daylight.com). Which may be of big help for representing libraries. ----------------------------------------------------------------------- From: "Malcolm A. Cline" If you will send me a FAX number, I will FAX you an application note using our software to build a combinatorial library. The library is a lead explosion around a single ACE (Angiotensin Converting Enzyme) inhibitor. (Remark: Unfortunately, I haven't got this yet.) ----------------------------------------------------------------------- From: Ronald D Ferguson Additional work on the subject which you address was expressed in an article by Dr. Martin from Chiron. In this J. Med. Chem. , 1995, Vol.38, 9, 1431-1436 article, Dr. Martin explained a algorithm they devised to define the "molecular diversity" of a combinatorial chemical library. As far as computational searches for structural diversity, "Chem-X" from Chemical Design as well as others have commercially available packages which will allow for such a "combinatorial chemical" search. These packages have publications of the theory and experiments which lead to the "final" programs. I can point you toward some of these references later if you wish, but I suggest that you look at the past four years of the Journal of Computer-Aided Molecular Design and the Journal of Molecular Graphics. Do a search (CAS or other) and pay attention to descriptors of "molecular shape", "3 dimensional data bases" and "structure retrieval systems". Names associated with these articles include the following: Chris Ho Garland Marshall Guy Bemis Irwin Kuntz Andrew Poirrette Peter Willett Zlatko Mihalic David ClarkShaun Jordan Andrew Leach R. Nilakantan N. Bauman R. Venkataraghavan Gustavo Arteca -------------------------------------------------------------------- Thanks to all you wrote to me. Best regards, Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| "Es irrt der Mensch, Lehrstuhl II f. Mathematik |\ \ | || solang er strebt. Universitaet Bayreuth | \ \ | || ... | \ \ | || Doch nur wer immer strebend 95440 Bayreuth | \ \\ || sich bemueht, denn koennen Germany | \ \\ || wir erloesen." Tel. +49 (921) 553386 | \ \\ || Goethe Fax +49 (921) 553385 | \-------|| +---------------+ **** Do you know MOLGEN? **** http://btm2xd.mat.uni-bayreuth.de/molgen **** From xiaopeng@astro.ocis.temple.edu Thu Jan 25 11:07:06 1996 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id KAA28393; Thu, 25 Jan 1996 10:59:54 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id KAA29533; Thu, 25 Jan 1996 10:59:41 -0500 (EST) Date: Thu, 25 Jan 1996 10:59:39 -0500 (EST) From: Peking To: ccl Subject: Summary--Gaussian IRC calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear nettlers, Several days ago, I posted a problem about Gaussian92 or 94 IRC calculation. And wondering if it is a bug. Due to some of my typing error, I misguided some people to the typo and thanks for their answers. Actually the problem is NOT anything missing from my command file. Although the problem has been solved, I still do not know what's wrong with it. Thanks to Stefan FAn, Magda Wajrak, Mike Frisch, Mori Seiji and Dr. Doug Fox for their reply. I ran IRC before using G92 and has no problem, so this time I am wondering why it always give me error termination. Well, I should talk about the solution. Mori Seiji suggested me copy the .chk file and run IRC in 2 separate calculation. one include "forward" option in IRC and another include "reverse". I used this and solved the problem. Dr. Doug Fox suggested me include "Geom=(coord, checkpoint) in the command file and he run this on his computer. Since I used "forward" and "reverse" option and solved the problem, I did not try this. And I still don't know why "geom=checkpoint" does not work, but "geom=(coord, checkpoint) will work, why spliting the IRC calculation into 2 separate will work, combining them together does not work. It seems it is not the probelm of memory or space since I have run a much bigger IRC problem at MP2 level and had no problem. Thanks again! xiaopeng ======================================================= Chemistry Graduate student 215-2047149(office) 215-5357188(home) xiaopeng@astro.ocis.temple.edu ====================================================== From nash@chem.wisc.edu Wed Jan 24 14:14:24 1996 Received: from audumla.students.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id OAA11226; Wed, 24 Jan 1996 14:14:21 -0500 Received: from caseyir by audumla.students.wisc.edu; id NAA130594; 8.6.9W/42; Wed, 24 Jan 1996 13:14:11 -0600 Date: Wed, 24 Jan 1996 13:14:11 -0600 Message-Id: <199601241914.NAA130594@audumla.students.wisc.edu> X-Sender: jrnash@students.wisc.edu (Unverified) X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "John R. Nash" Subject: From one structure to another Status: R I am seeking a utility that will take as input the cartesian coordinates of compounds A and B and generate x number of intermediate structures in between the two by interpolation (i.e. morphing from one structure to the other). I know that some packages will do this sort of thing for "linear synchronous transit" calculations, but I need the input files for a computation where this is not included. (The molecule is way too big for GAUSSIAN... could the program perhaps be convinced to calculate the coordinates w/o running the qm calculation on them?) This seems like an simple enough utility to write, but my guess is that it must have been done by someone... Thanks in advance! -john nash -==-John R. Nash-==-nash@chem.wisc.edu-==-Dept of Chemistry, UW-Madison-==- From sschulz@chemie.fu-berlin.de Thu Jan 25 07:28:07 1996 Received: from weasel.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/950822.1) id HAA24696; Thu, 25 Jan 1996 07:27:30 -0500 Received: by weasel.chemie.fu-berlin.de (1.37.109.16/16.2) id AA153342844; Thu, 25 Jan 1996 13:27:24 +0100 Date: Thu, 25 Jan 1996 13:27:24 +0100 (MEZ) From: Stefan Schulz To: chemistry@www.ccl.net Subject: dipole moment vector in MOLPRO94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Dear CCLers ! I have a question concerning the direction of the dipole moment vector of CASSCF excited states computed by MOLPRO94. The situation is the following: I have a molecule in C3v symmetry: ATOMIC COORDINATES NR ATOM CHARGE X Y Z 1 NA 11.00 0.000000000 0.000000000 -2.555725461 2 N 7.00 0.000000000 0.000000000 3.344274539 3 H 1.00 -0.909712280 -1.575667890 3.944274539 4 H 1.00 -0.909712280 1.575667890 3.944274539 5 H 1.00 1.819424561 0.000000000 3.944274539 Due to the fact that MOLPRO94 can only handle abelian groups I am forced to do my calculations using Cs symmetry. Nevertheless the full point group of the molecule is still C3v and by what I have learned about symmetry the dipole moment vector should in this case point along the molecular (z) axis. Since the dipole moment vector is a physical observable as such it can not depend on the point group used for your calculations but must only depend on the actual point group of the molecule. As it turns out, some of the excited CASSCF states show a dipole moment vector in the (x,z) plane with a component x different from 0 ! For example the fifth state in A' symmetry has a CASSCF dipole moment vector -0.54844048 0.00000000 -2.76337735 a.u. Interestingly enough the second state in A" symmetry which due to the correlation of the twodimensional E irrep of the C3v group with the A' and A" irreps of the Cs group should be energetically degenerate with the fifth state in A' has a CASSCF dipole moment vector of 0.54844057 0.00000000 -2.76337738 a.u. The strange thing is that the CASSCF procedure converges in three iterations and gives no warnings, so the choice of active orbitals and optimized states should be ok. Until now the only explanation I have come up with is that although the convergence threshold for the energy is met the wavefunction still somehow has some components left which give rise to the x-component of the dipole moment vector. Has any MOLPRO94 user experienced this kind of problems before? Have I run into a bug or am I missing something? Any help or hint will be greatly appreciated. I'll summarize to the list. To make things more transparent I include a sample input file showing the choice of active electrons, etc.: ***,NaNH3 excited states, CASSCF method !------------------------------------------- ! Set limit on dynamic memory !------------------------------------------- memory,18,m ! 18 000 000 floating point words !------------------------------------------- ! Define CASSCF procedures !------------------------------------------- proc my_scf text,ROHF rhf; ! restricted open shell HF wf,21,1,1; ! wavefunction spatial and spin symmetry occ,9,2; ! orbital occupation pattern start,0; ! use eigenvectors of h as guess save,2130.2; ! save orbitals at record 2130 of file 2 orbprint,15; ! print all occupied orbitals and 8 ! additional virtual orbitals of every ! symmetry species endproc proc my_casscf mcscf; ! casscf occ,17,6; ! occupied orbitals core,7,2; ! frozen-core orbitals closed,7,2; ! closed-shell orbitals config,csf; ! use CSFs instead of determinants save,,2150.2; ! save CI vectors for use in subsequent MRCI wf,21,1,1;state,9; ! request nine states of symmetry 1 wf,21,2,1;state,4; ! request four states of symmetry 2 start,2130.2; ! start with scf orbitals natorb,2140.2,ci; ! print natural orbitals and CI coefficients thresh,0.005; ! threshold for printing CI coefficients endproc !------------------------------------------- ! Open punch file, overwriting any previous ! information on this file !------------------------------------------- punch,sample.pun,new !------------------------------------------- ! Print molecular orbitals !------------------------------------------- print, orbital !------------------------------------------- ! Z-matrix input !------------------------------------------- geometry={y; Na; N,Na,r; H1,N,rb,Na,phi; H2,N,rb,Na,phi,H1,120.0; H3,N,rb,Na,phi,H1,240.0} !------------------------------------------- ! VTZ basis set augmented by: ! ! o two s-type diffuse functions ! o two p-type diffuse functions ! o one d-type polarization function ! o two d-type diffuse functions !------------------------------------------- basis={spdf,Na,vtz;c; spdf,N,vtz;c; spd,H,vtz;c; s,Na,0.010; s,Na,0.005; p,Na,0.027; p,Na,0.010; d,Na,0.160; d,Na,0.010; d,Na,0.004} !------------------------------------------- ! assign values to internal coordinates !------------------------------------------- rb = 1.9158042 bohr ! N-H bond length r0 = 3.50 bohr ; dr = 0.40 bohr ; nr = 28 x0 = 0.60 bohr ; dx = 0.10 bohr ; nx = 1 !------------------------------------------- ! loop over all geometries !------------------------------------------- do i = 1,nr r = r0 + (i-1)*dr ! value of dissociation coordinate do j = 1,nx x = x0 + (j-1)*dx ! value of inversion coordinate phi = acos(-x/rb) degree ! Na-N-H internuclear angle int; !invoke integral program my_scf; !call scf procedure my_casscf; !call casscf procedure delete,3; enddo ! end of loop over dissociation coordinate enddo ! end of loop over inversion coordinate Regards Stefan =-=-=-=-this message is transmitted on 100 % recycled electrons-=-=-=-= | | | | sschulz@chemie.fu-berlin.de | Stefan Schulz | | Tel. ++49/30/838 5384 | FU Berlin - Theoretical Chemistry | | ++49/30/838 2351 | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From jkl@ccl.net Thu Jan 25 13:37:08 1996 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA01816; Thu, 25 Jan 1996 13:25:48 -0500 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id NAA14374; Thu, 25 Jan 1996 13:25:46 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id NAA02345; Thu, 25 Jan 1996 13:25:45 -0500 Date: Thu, 25 Jan 1996 13:25:45 -0500 Message-Id: <199601251825.NAA02345@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Budget pissing match and us in US Cc: jkl@ccl.net Dear Netters, I am sending it to the list knowing that it is not in the scope of CCL. But just to make some of you realize. Please do not discuss it on the list, but act one way or the other, or do nothing if you so please or if it does not concern you. Thanks to Mary Jo Ondrechen to point to this: > The ACS Federal Funding Networks has issued an appeal > for all to contact the folks in Washington becasue: > 1) Funding runs out for the NSF on January 26. > 2) While the NIH got a 5.7% increase over FY 1995, the > NSF has not been treated so well. > The ACS FFN asks everyone to contact your representatives > by January 25. Fax numbers are available upon request > to the ACS FFN. For more information, contact nsfnet@acs.org > > All proposal are about to get put on hold, and a protracted > shutdown could put existing grants in trouble. THere is > a perception in Washington that the NSF is not so important. > (i.e., that the scientific community has been silent about Jan Labanowski jkl@ccl.net From arthur@csb0.IPC.PKU.EDU.CN Thu Jan 25 21:07:13 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id VAA08732; Thu, 25 Jan 1996 21:02:18 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA04650; Fri, 26 Jan 96 09:53:22 -0800 Date: Fri, 26 Jan 1996 09:53:19 -0800 (PST) From: Arthur Wang To: CCL mailing list Cc: drug.dna@sci.port.ac.uk, molmodel@net.bio.net Subject: Chemical Structures Wanted Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Please just tell me the topological structures of these two Nucleosides: dDAPR (C16H16O3N6) and F6ddP (C10H13O2N4F). They have cost me much time but I could not find them in the library. Any expert? Thanks in advance. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/home.htm _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/