From owner-chemistry@ccl.net Tue Oct 10 02:54:20 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id CAA05738; Tue, 10 Oct 1995 02:44:03 -0400 Received: from rugch4.chem.rug.nl for tieleman@chem.rug.nl by bedrock.ccl.net (8.6.10/950822.1) id CAA29439; Tue, 10 Oct 1995 02:44:01 -0400 From: Received: from rugmd10.chem.rug.nl by rugch4.chem.rug.nl with SMTP (1.38.193.4/16.2) id AA26704; Tue, 10 Oct 1995 07:44:02 +0100 Received: by rugmd10 (940816.SGI.8.6.9/930416.SGI) id HAA14084; Tue, 10 Oct 1995 07:45:06 +0100 Date: Tue, 10 Oct 1995 07:45:06 +0100 Message-Id: <199510100645.HAA14084@rugmd10> To: chemistry@ccl.net Subject: dppc Could anyone provide me with the crystalcoordinates of dipalmitoylphosphatidylcholine (DPPC) ? I can't find them in the CSD or in another dbase I have access too. Thanks. Peter -- email: tieleman@chem.rug.nl adress: Dept. of Biophysical Chemistry telephone: 31-50-634338 Nijenborgh 4 fax: 31-50-634800 9747 AG Groningen The Netherlands From owner-chemistry@ccl.net Tue Oct 10 03:54:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA06405; Tue, 10 Oct 1995 03:45:28 -0400 Received: from uni-paderborn.de for GF@chemie.uni-paderborn.de by bedrock.ccl.net (8.6.10/950822.1) id DAA29672; Tue, 10 Oct 1995 03:45:23 -0400 Received: from linux.uni-paderborn.de (root@linux.uni-paderborn.de [131.234.12.32]) by uni-paderborn.de (8.6.12/8.6.12) with ESMTP id IAA25336 for ; Tue, 10 Oct 1995 08:44:39 +0100 Received: from physik.uni-paderborn.de (physik [131.234.242.11]) by linux.uni-paderborn.de (8.7/8.7) with SMTP id IAA01429 for ; Tue, 10 Oct 1995 08:44:40 +0100 Received: From FB6/WORKQ1 by physik.uni-paderborn.de via Charon-4.0A-VROOM with IPX id 100.951010084309.448; 10 Oct 95 08:44:38 +0100 Message-ID: From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: chemistry@ccl.net Date: Tue, 10 Oct 1995 08:42:52 GST Subject: Display of electron densities Priority: normal X-mailer: Pegasus Mail for Windows (v2.0-WB3) Does anybody know of a program that reads atomic coordinates and charges (e.g from AM1 calculation) and displays the result as 3D globular graphic? Answers will be posted to the list. Thanks Gregor Fels Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de From owner-chemistry@ccl.net Tue Oct 10 04:24:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA06680; Tue, 10 Oct 1995 04:18:33 -0400 Received: from techunix.technion.ac.il for chr07pa@techunix.technion.ac.il by bedrock.ccl.net (8.6.10/950822.1) id EAA29738; Tue, 10 Oct 1995 04:18:27 -0400 Received: (from chr07pa@localhost) by techunix.technion.ac.il (8.6.12+/8.6.10) id KAA29235; Tue, 10 Oct 1995 10:17:54 +0200 Date: Tue, 10 Oct 1995 10:17:49 +0200 (EET) From: Pauncz Ruben To: LIST CC Subject: The Symmetric Group in Quantum Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to bring to your attention the following new book: The Symmetric Group in Quantum Chemistry Ruben Pauncz The use of the symmetric group in the quantum chemical treatment of the structure of atoms, molecules and solids has central importance. This is the first book which gives a systematic treatment of the subject. It is self-contained, it starts with the conventional Slater determinant approach, it proceeds to the basic notions for the representation of the symmetric group and the construction of spin-eigenfunctions. The heart of the book is in the chapter dealing with spin-free quantum chemistry. It shows the great interpretation value of this treatment and shows that computationally this method is not inferior to the conventional treatment. The three last chapters contain the unitary group approach, the symmetric group approach and the spin-coupled valence bond method. A fairly extensive bibliography concludes the book. The book can be used as an textbook for a one semeter graduate course or for independent study by an advanced student of physical chemistry or physics. Table of contents Chapter 1 The quantum mechanical background..............1 1.1 Introduction...........................................1 1.2 Spin-free Hamiltonian..................................1 1.3 The antisymmetry principle.............................3 1.4 Atomic and molecular orbitals..........................4 1.5 Slater determinant.....................................5 1.6 The self-consistent-field method.......................7 1.7 Configuration interaction method.......................8 1.8 Slater-Condon rules...................................10 1.9 Lowdin rules..........................................12 Chapter 2 The Symmetric Group...........................19 2.1 Introduction..........................................19 2.2 Permutations..........................................19 2.3 The symmetric group...................................20 2.4 Cyclic permutation....................................20 2.5 Classes of the symmetric group........................23 2.6 Subgroups of the symmetric group......................25 2.7 Double cosets.........................................27 Chapter 3 Representation of SN..........................31 3.1 Reps of the symmetric group...........................31 3.2 Young tableaux........................................32 3.3 Young's orthogonal representation.....................36 3.4 The branching law of the symmetric group..............38 3.5 The conjugate representation..........................40 3.6 The coset representation..............................42 3.7 Decomposition of the coset representation.............46 3.8 Characters of the symmetric group.....................48 3.9 Calculation of the Characters.........................58 3.10 The subgroup S2 x S_2 ......x S2.....................62 3.11 Appendix.1.......................................... 63 Chapter 4 The symmetric group algebra...................67 4.1 Algebraic notions.....................................67 4.2 Class operators.......................................69 4.3 Matric basis of the group algebra.....................72 4.4 Matric basis for the centrum of the algebra...........75 4.5 The Young operator basis..............................79 Chapter 5 Spin eigenfunctions...........................95 5.1 Introduction..........................................95 5.2 Construction of spin eigenfunctions...................95 5.3 The genealogical construction.........................96 5.4 The branching diagram.................................98 5.5 Reps of the SN generated by the spinfns..............102 5.6 Yamanouchi-Kotani method for the reps................105 5.7 Branching diagram fns and Young tableaux.............108 5.8 Serber spin functions................................112 5.9 Projected spin eigenfunctions........................115 5.10 Spin-paired spin eigenfunctions.....................123 5.10.1 Correspondence between spin-paired functions and Young tableaux...................................131 Chapter 6 Spatial functions............................135 6.1 Antisymmetric wavefunction...........................135 6.2 Decomposition of the wavefunction....................137 6.3 Reps of SN by the spatial functions.................138 6.4 Branching diagram functions..........................139 6.5 Serber wavefunction..................................141 6.6 Projected wavefunction...............................149 6.7 Valence bond wavefunction............................152 Chapter 7 Spin free quantum chemistry..................157 7.1 Introduction.........................................157 7.2 Orbital product functions............................157 7.3 Invariance group of the primitive ket................158 7.4 Spin free exclusion principle........................161 7.5 Structure projections................................163 7.5.1 The pair diagram...................................163 7.5.2 The pair operators.................................165 7.5.3 Spin free pair functions...........................167 7.5.4 Pair projections in the function space.............168 7.5.5 Spin free exclusion principle for structure projections........................................169 7.6 Spin free counterpart of A Phi Vk...................170 7.7 Spin free counterpart of the projected fn............175 7.8 Gallup's tableau operators...........................180 7.9 Calculation of the Pauling numbers...................183 7.10 Li's algorithm......................................186 Chapter 8 Unitary group approach.......................195 8.1 Introduction.........................................195 8.2 Basic notions........................................195 8.3 Tensor space.........................................201 8.4 Model Hamiltonian....................................203 8.5 Reps of the unitary group............................206 8.6 The branching law of the unitary group...............209 8.7 Representation matrices of the generators............210 8.8 Weyl tableaux........................................217 8.9 Electronic Gel'fand state............................219 8.10 Paldus arrays.......................................221 8.11 Graphical unitary group approach ...................233 8.12 Direct configuration interaction method.............248 Chapter 9 Symmetric group approach in CI...............253 9.1 Introduction.........................................253 9.2 Representation matrices..............................254 9.3 Sarma and Rettrup algorithm..........................258 9.4 Duch and Karwowski algorithm.........................267 9.5 Symmetric group graphical approach...................274 Chapter 10 Spin-coupled functions.......................281 10.1 Introduction........................................281 10.2 Historical development..............................282 10.3 Spin-coupled wavefunctions..........................286 10.4 SCVB functions......................................289 10.5 Core-valence s-c wavefunction.......................290 Bibliography..............................................295 Author index..............................................321 Subject index.............................................327 CRC Press, Inc. Boca Raton, Florida June 1995 ISBN 0-8493-8291-2 330 pages U.S. $ 110.00 Outside U.S. $ 132.00 *-------------------------------------------* | Dr. Ruben Pauncz, Professor Emeritus | | Department of Chemistry | | Technion - Israel Institute of Technology | | Haifa 32000, Israel | | | | CHR07PA@TECHNION.TECHNION.AC.IL | | Telephone: +972-4-293743 | | Fax: +972-4-233735 | *-------------------------------------------* From mcblimts@leonis.nus.sg Tue Oct 10 05:09:22 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id FAA07424; Tue, 10 Oct 1995 05:04:04 -0400 Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id RAA28283 for ; Tue, 10 Oct 1995 17:03:55 +0800 Received: from ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id RAA16894 for ; Tue, 10 Oct 1995 17:03:53 +0800 Date: Tue, 10 Oct 1995 17:03:53 +0800 Message-Id: <199510100903.RAA16894@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: mcblimts@leonis.nus.sg (Lim Teck Sin) Subject: Allosteric effects of macromolecules X-Mailer: Hi, Does anyone know of people/groups which are investigating allosteric effects of macromolecules (eg: haemoglobin)? Thanks. best regards - teck sin From ldw@csb0.IPC.PKU.EDU.CN Tue Oct 10 09:09:27 1995 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id JAA10312; Tue, 10 Oct 1995 09:05:10 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA07598; Mon, 10 Oct 94 21:05:40 -0700 Date: Mon, 10 Oct 1994 21:05:39 -0700 (PDT) From: ldw To: chemistry@www.ccl.net Subject: Need small peptide structure data Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I want to collect small peptide(length less then 10 peptide) structure(or comformation) data either detimined by X-ray crystallography or NMR. References about it are also welcome. Thanks in advance, Dawei ----------< *** Dawei LIN *** >---------------- Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 P.R.China Phone: 86-10-2501490 Fax: 86-10-2501725 Email: ldw@ipc.pku.edu.cn ldw@pschnetware.pku.edu.cn URL: http://www.ipc.pku.edu.cn/ldw/ldw.htm ------------------------------------------------ From owner-chemistry@ccl.net Tue Oct 10 09:39:25 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA11055; Tue, 10 Oct 1995 09:30:50 -0400 Received: from Princeton.EDU for jimreho@phoenix.Princeton.EDU by bedrock.ccl.net (8.6.10/950822.1) id JAA01243; Tue, 10 Oct 1995 09:30:48 -0400 Received: from ponyexpress.Princeton.EDU by Princeton.EDU (5.65b/2.122/princeton) id AA25602; Tue, 10 Oct 95 09:26:51 -0400 Received: from phoenix.Princeton.EDU (jimreho@phoenix.Princeton.EDU [128.112.128.43]) by ponyexpress.Princeton.EDU (8.6.12/8.6.12) with ESMTP id JAA22434 for ; Tue, 10 Oct 1995 09:26:50 -0400 From: "James H. Reho" Received: (jimreho@localhost) by phoenix.Princeton.EDU (8.6.12/8.6.12) id JAA14138 for chemistry@ccl.net; Tue, 10 Oct 1995 09:26:47 -0400 Date: Tue, 10 Oct 1995 09:26:47 -0400 Message-Id: <199510101326.JAA14138@phoenix.Princeton.EDU> To: chemistry@ccl.net Subject: Li2 triplet dimers Hello! I have written before about a problem with using Gaussian 92 to reproduce a HF calculation of the triplet Li2 ground state. This state should be totally repulsive: however,my function reaches a minimum and then energy RISES with increasing internuclear distance. Physically, this doesn't seem possible for the HF of this state (and I know that the state IS totally repulsive). I have tried using UHF as well as ROHF and the basis sets 6-31G as well as 6-311G**. I don't know what else to do! Any input would be helpful... Thanks, jimreho@phoenix.princeton.edu From henk@qsar.ritox.dgk.ruu.nl Tue Oct 10 09:40:19 1995 Received: from qsar.ritox.dgk.ruu.nl for henk@qsar.ritox.dgk.ruu.nl by www.ccl.net (8.6.10/950822.1) id JAA11236; Tue, 10 Oct 1995 09:37:07 -0400 From: Received: by qsar.ritox.dgk.ruu.nl (MX V4.0 VAX) id 13; Tue, 10 Oct 1995 14:35:12 CET Date: Tue, 10 Oct 1995 14:35:11 CET To: chemistry@www.ccl.net Message-ID: <00997AA6.11A02C80.13@qsar.ritox.dgk.ruu.nl> Subject: configuration interaction in semiemp. schemes? Dear all, I have what I think is a simple (minded) question: As far as my limited knowledge goes, it is generally true that in ab initio schemes, calculated heats of formation get 'better' as more electron correlation is taken into account -- either through configuration interaction, use of Moeller-Plesset schemes or other technique. What I'd like to know is: how does this apply to semi-empirical schemes? My personal 'feeling' is that, since SE schemes were parameterized to closely reproduce experimental heats of formation (for a limited set of training compounds) in the single determinant form, any correlation scheme lowering this energy will lead to larger (average) deviations from experimental values -- if this is true, one would have to use the HoF from a single determinant calculation, while certain other characteristics might be better calculated using CI schemes (thinking of UV spectra in particular). Is this correct? ==========One man's FF@ state-of-mind is another man's Hydropsyche!=========== | Henk Verhaar | e-mail: henk@qsar.ritox.dgk.ruu.nl | | Research Institute of Toxicology | | | Environmental Toxicology Section | phone: +31 30 535338 | | Utrecht University, the Netherlands | fax: +31 30 535077 | ============================================================================== From owner-chemistry@ccl.net Tue Oct 10 10:54:29 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA13591; Tue, 10 Oct 1995 10:54:01 -0400 Received: from sgi.sgi.com for mberger@strider.engr.sgi.com by bedrock.ccl.net (8.6.10/950822.1) id KAA02317; Tue, 10 Oct 1995 10:53:59 -0400 Received: from strider.engr.sgi.com by sgi.sgi.com via ESMTP (950405.SGI.8.6.12/910110.SGI) id HAA16254; Tue, 10 Oct 1995 07:53:57 -0700 Received: by strider.engr.sgi.com (940816.SGI.8.6.9/940406.SGI.AUTO) id HAA22766; Tue, 10 Oct 1995 07:53:56 -0700 From: "Mark Berger" Message-Id: <9510100753.ZM22764@strider.engr.sgi.com> Date: Tue, 10 Oct 1995 07:53:56 -0700 In-Reply-To: jstewart@fai.com (Dr. James Stewart) "MOPAC 93 and MOPAC 7" (Jun 24, 12:51pm) References: <9306241951.AA03701@fujitsu.fai.com> X-Mailer: Z-Mail-SGI (3.2S.2 10apr95 MediaMail) To: chemistry@ccl.net, jstewart@fai.com (Dr. James Stewart) Subject: Re: MOPAC 93 and MOPAC 7 Cc: dzirl@sgi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii -- -------------------------------------------------------------------------------- Mark Berger Chemistry Market Manager Silicon Graphics Computer Systems, Inc. phone: (415) 390-1772 Mailstop 24U-970 fax: (415) 933-0823 2011 N. Shoreline Blvd. email: mberger@sgi.com Mountain View, CA 94039-7311 WWW: http://www.sgi.com/ChemBio -------------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Oct 10 11:54:26 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA15253; Tue, 10 Oct 1995 11:43:27 -0400 Received: from hermes for A.T.Yagnik@exeter.ac.uk by bedrock.ccl.net (8.6.10/950822.1) id LAA02863; Tue, 10 Oct 1995 11:43:13 -0400 From: Received: from cen by hermes via ESMTP (QAA04982); Tue, 10 Oct 1995 16:42:33 +0100 Message-Id: <29141.199510101542@cen> Subject: Book/review articles on forcefields To: chemistry@ccl.net Date: Tue, 10 Oct 1995 16:42:32 +0100 (BST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1024 Hi, Does anyone out there know of a good book or review article on forcefields? In particular, my colleagues are interested in any articles which may aid in choosing the 'best' forcefield for a particular problem - if such a thing exists (I know it is rather subjective, but they would appreciate any leads). Thank you for your time. Regards, Tosh -- =============================================================================== Asutosh T Yagnik, Tel: (+44) 1392 263451 Protein Structure Group, Fax: (+44) 1392 263434 Department of Chemistry, Email: ATYagnik@exeter.ac.uk University of Exeter, * * WWW: http://www.exeter.ac.uk/ Stocker Road, Exeter. EX4 4QD. UK. > ~ATYagnik/ATYagnik \__/ {All opinions are my own!} "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi =============================================================================== From karney@euclid.chem.washington.edu Tue Oct 10 12:09:28 1995 Received: from euclid.chem.washington.edu for karney@euclid.chem.washington.edu by www.ccl.net (8.6.10/950822.1) id LAA15550; Tue, 10 Oct 1995 11:55:50 -0400 Received: by euclid.chem.washington.edu (AIX 3.2/UCB 5.64/4.03) id AA19032; Tue, 10 Oct 1995 08:55:30 -0700 Date: Tue, 10 Oct 1995 08:55:30 -0700 From: karney@euclid.chem.washington.edu (Bill Karney) Message-Id: <9510101555.AA19032@euclid.chem.washington.edu> To: chemistry@www.ccl.net Subject: unsubscribe Please unsubscribe From chipot@boltzmann.arc.nasa.gov Tue Oct 10 12:24:29 1995 Received: from boltzmann.arc.nasa.gov for chipot@boltzmann.arc.nasa.gov by www.ccl.net (8.6.10/950822.1) id MAA16154; Tue, 10 Oct 1995 12:23:23 -0400 Message-Id: <199510101623.MAA16154@www.ccl.net> Received: by boltzmann.arc.nasa.gov (1.38.193.4/16.2) id AA21294; Tue, 10 Oct 1995 09:34:26 -0700 From: Chris Chipot Subject: Changing of Address To: chemistry@www.ccl.net Date: Tue, 10 Oct 95 9:34:25 PDT Mailer: Elm [revision: 70.85] Starting today, my new e-mail address will be: chipot@max.arc.nasa.gov instead of: chipot@boltzmann.arc.nasa.gov _______________________________________________________________________ Chris Chipot Phone: (415) 604-5496 NASA/Ames Research Center Fax: (415) 604-1088 MS 239-4 Moffett Field, CA 94035-1000 E-mail: chipot@max.arc.nasa.gov _______________________________________________________________________ From dimitris@3dp.com Tue Oct 10 13:09:30 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/950822.1) id NAA17451; Tue, 10 Oct 1995 13:03:46 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA17162; Tue, 10 Oct 95 13:06:41 -0400 Received: by europa.3dp.com (931110.SGI) id AA29064; Tue, 10 Oct 95 13:04:59 -0400 From: "Dimitris Agrafiotis" Message-Id: <9510101304.ZM29062@europa.3dp.com> Date: Tue, 10 Oct 1995 13:04:58 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Need Pauling's formula for VDW radii Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Does anyone know Pauling's formula for estimating the van der Waals radius of an atom based on its atomic/ionic radius? It's a simple formula which (I think) is given in his book "The Nature of the Chemical Bond", but for some reason hasn't made it into the physical chemistry textbooks that I have access to. Your help will be greatly appreciated. Thanks, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From owner-chemistry@ccl.net Tue Oct 10 14:09:29 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA19184; Tue, 10 Oct 1995 14:01:23 -0400 Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by bedrock.ccl.net (8.6.10/950822.1) id OAA04544; Tue, 10 Oct 1995 14:01:21 -0400 From: Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HWA0B3N94G95MUTX@phem3.acs.ohio-state.edu>; Tue, 10 Oct 1995 14:00:51 EDT Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 2964; Tue, 10 Oct 1995 13:59:06 -0400 Date: Tue, 10 Oct 1995 13:43:41 -0400 (EDT) Subject: Reaction Paths ?? To: chemistry@ccl.net Message-id: <01HWA0BAQB8895MUTX@phem3.acs.ohio-state.edu> Organization: East Tennessee State University Content-transfer-encoding: 7BIT CCL Users: I would like to use MOPAC to investigate the reaction of H2 with a planar molecule. Since one is allowed just one reaction coordinate, I set up the problem as follows: XX XX 2.5 -1 0.0 1 H .5 1 90.0 1 0.0 0 2 1 H .5 1 90.0 1 180.0 0 2 1 3 etc. The planar molecule is fastened to the first dummy atom. My idea was to shorten the distances between to the two dummy atoms to study the reaction. My output is very strange. The H2 hardly moves. Each cycle of the reaction shows the shortened distance I've selected, but the xyz coordinates show the H2 out at approximately the 2.5 A starting distance. Does anyone have any hints on how to vary this approach distance properly? Can one indeed use dummy atoms in a reaction path? If so then what is wrong? Regards, Dave Close. From owner-chemistry@ccl.net Tue Oct 10 14:24:30 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA19555; Tue, 10 Oct 1995 14:14:15 -0400 Received: from ns2.harvard.edu for marty@ionchannel.med.harvard.edu by bedrock.ccl.net (8.6.10/950822.1) id OAA04756; Tue, 10 Oct 1995 14:14:11 -0400 Received: by ns2.harvard.edu (5.65/DEC-Ultrix/4.3) id AA03871; Tue, 10 Oct 1995 14:14:10 -0400 Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA05000; Tue, 10 Oct 95 14:06:47 EDT Received: from [134.174.159.173] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:chemistry@ccl.net id AA09449; Tue, 10 Oct 95 14:14:08 -0700 Date: Tue, 10 Oct 95 14:14:08 -0700 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: marty@ionchannel.med.harvard.edu (Martin J. Gallagher) Subject: development of antiviral agents Hello, I am beginning to think about possible postdoc projects in which I could apply my PhD experience in protein chemistry/phramacology to studies of infectious diseases. Therefore, I was hoping someone in this group could point me to a current review article that would highlight important questions concerning the development of antiviral agents. Medline gives me many hits, so advice from experienced researchers would help me focus. Thank you, Marty Gallagher ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave http://ionchannel.med.harvard.edu/~marty Boston, MA 02115 =========================================================================== Finger, or WWW for PGP Public Key =========================================================================== -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From smb@smb.chem.niu.edu Tue Oct 10 15:54:31 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id PAA22608; Tue, 10 Oct 1995 15:48:13 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA08283 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Tue, 10 Oct 1995 14:48:22 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA13568; Tue, 10 Oct 95 13:57:20 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA22046; Tue, 10 Oct 95 13:57:20 -0500 Date: Tue, 10 Oct 95 13:57:20 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9510101857.AA22046@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: ECCC2 Registration Open The Second Electronic Computational Chemistry Conference will take place from Nov. 1 - 30, 1995. There will be 65 papers covering a wide cross-section of computational chemistry. The conference will be held entirely on the Internet. You can access the conference in two ways. If you do not wish to partake in the discussions, which will be handled by www forms (and not via email), you can get to the conference home page at http://hackberry.chem.niu.edu/ECCC2/homepage.html If you do wish to also participate in the discussions, please register for the conference at http://hackberry.chem.niu.edu/cgi-bin/discuss.cgi This address will also be your entrance into the conference after you register. Please note that the conference officially begins on November 1, 1995. On that date, the full text of the papers will be released. Right now, we are making available only the abstracts. Information on the conference can be obtained at http://hackberry.chem.niu.edu/ECCC2/ Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From gford@post.smu.edu Tue Oct 10 17:24:31 1995 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.6.10/950822.1) id RAA24845; Tue, 10 Oct 1995 17:24:20 -0400 Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.1) id ; Tue, 10 Oct 95 16:24 CDT Message-Id: Date: Tue, 10 Oct 95 16:24 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: Chemistry@www.ccl.net Subject: CCL:Hydrogenation reaction path Dave Close writes: > I would like to use MOPAC to investigate the reaction of H2 with a > planar molecule. Since one is allowed just one reaction coordinate, > I set up the problem as follows: > > XX > XX 2.5 -1 0.0 1 > H .5 1 90.0 1 0.0 0 2 1 > H .5 1 90.0 1 180.0 0 2 1 3 > etc. > > The planar molecule is fastened to the first dummy atom. My idea > was to shorten the distances between to the two dummy atoms to study > the reaction. My output is very strange. The H2 hardly moves. Each > cycle of the reaction shows the shortened distance I've selected, but > the xyz coordinates show the H2 out at approximately the 2.5 A starting > distance. The trouble is you have too many degrees of freedom. You will notice that as the reaction coordinate changes the distances and angles defining the hydrogen atoms (which you have defined as variables) simply change to allow the H2 to remain in its minimum energy position. Mopac does allow the equivalent of two reaction coordinates via the GRID keyword. However, unless you restrict yourself to special symmetrical situations even that is not enough. In the absence of symmetry this is at least a three "reaction coordinates" problem. There are two C-H distances and the H-H distance, all of which change substantially along the reaction path. Any "reaction path" treatment using less than this number must employ some kind of arbitrary relationship between them. Do you really want to visualize the potential surface in this much detail? If you are simply trying to locate approximate transition state geometries you could probably make estimates that are good enough to use with one of the several refinement options in MOPAC (NLLSQ, EF, etc) in other ways. Withough knowing what reaction you are studying its hard to suggest exactly how to go this. If, for exmaple, you are adding H2 to a multiple bond you could probably generate a good enough trial t.s. by interpolating between the geometries of the product and one with an intact H2 above the double bond at about the van der Waals distance. This could be done manually, or via the SADDLE option. Some experimentation might be required. However, with one t.s. in hand it could be used as a template for the remainder. Hope this helps. > ============================================================================ George P. Ford | email: gford@mail.smu.edu Department of Chemistry | telephone: (214)768-2479 Southern Methodist University | fax: (214)768-4089 Dallas, Texas 75275 | ============================================================================ From owner-chemistry@ccl.net Tue Oct 10 18:54:32 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA26506; Tue, 10 Oct 1995 18:47:40 -0400 Received: from apolo.eafit.edu.co for efrt713@apolo.eafit.edu.co by bedrock.ccl.net (8.6.10/950822.1) id SAA07769; Tue, 10 Oct 1995 18:47:32 -0400 Received: by apolo.eafit.edu.co (5.65/25-eef) id AA13225; Tue, 10 Oct 95 17:05:15 -0400 Date: Tue, 10 Oct 1995 17:05:14 -0400 (EDT) From: FELIPE RENDON TRUJILLOREAL To: Chemistry@ccl.net. Cc: braendle@iac.unibe.ch Subject: Solar energy Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HI, I want to know some information about solar energy as fuel , if you have information please send me , or If you know were can I found that information send me the E/mail , this information is to work in a project for the school , they are working a lot of fuels like water,solar energy, alcohol and others Thank a lot I am waiting for your answer Felipe Rendon T Medellin ,Colombia From owner-chemistry@ccl.net Tue Oct 10 22:39:35 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA29836; Tue, 10 Oct 1995 22:30:17 -0400 Received: from dub-mail-svc-1.compuserve.com for 73171.2310@compuserve.com by bedrock.ccl.net (8.6.10/950822.1) id WAA08988; Tue, 10 Oct 1995 22:30:12 -0400 From: <73171.2310@compuserve.com> Received: from NULL (ad45-167.compuserve.com [199.174.163.167]) by dub-mail-svc-1.compuserve.com (8.6.10/8.6.9) with SMTP id WAA16233.; Tue, 10 Oct 1995 22:30:01 -0400 Date: Tue, 10 Oct 1995 22:30:01 -0400 Message-Id: <199510110230.WAA16233@dub-mail-svc-1.compuserve.com> To: chemistry@ccl.net Subject: a short survey/interview for chem. engineers Content-type: text/plain Content-length: 1558 X-Mailer: AIR Mosaic (16-bit) version 1.00.198.07 My name is Thomas Hess and I am a student at Champlin Park High School in Minnesota. I would appreciate it if you would answer a few questions about yourself and what you do. This information will only be reviewed by myself and will help me with my career project. Thank you very much! Send to: Thomas Hess or Kent Olson at 73171,2310@compuserve.com Thanks! 1. What is your name and e-mail address or phone number? 2. What is your official job title? 3. What did you recieve as a starting salary and what is your salary now? 4. What duties must you preform on an average day? 5. Do you enjoy your occupation? 6. What was(were) you major(s) and minor(s) in college? 7. What degree did you recieve and from where? 8. Do you have any comments on the quality of the program, teaching, or the facilities? 9. How long did it take you? 10. Have you had any further education? 11. Did your degree/college education prepare you for your job? 12. What are and have been your hobbies? 13. What subjects did you enjoy during high school? excell in? 14. Give a brief description of your personality. 15. What are your likes/dislikes? 16. Where do you feel this field is going? 17. Is there another field that you wish you had gone into? 18. What other fields do you see expanding or developing now and into the future (please be specific if possible)? 19. Any other information that you feel would be helpful? Send to: Thomas Hess or Kent Olson at 73171,2310@compuserve.com Thank you once again! I really appreciate this.