From KRUGER@che.und.ac.za Tue Feb 4 01:20:47 1997 Received: from Raven.und.ac.za for KRUGER@che.und.ac.za by www.ccl.net (8.8.3/950822.1) id BAA09222; Tue, 4 Feb 1997 01:05:39 -0500 (EST) Received: from che.und.ac.za (ChemFS1.ChE.und.ac.za [146.230.128.46]) by Raven.und.ac.za (8.8.3/8.7.3) with ESMTP id IAA12411 for ; Tue, 4 Feb 1997 08:05:24 +0200 (SAT) Received: from CHEMENG/SpoolDir by che.und.ac.za (Mercury 1.21); 4 Feb 97 08:05:24 +0200 Received: from SpoolDir by CHEMENG (Mercury 1.21); 4 Feb 97 08:04:58 +0200 From: "Mr HG Kruger" Organization: University of Natal - Durban To: CHEMISTRY@www.ccl.net Date: Tue, 4 Feb 1997 08:04:54 SAST Subject: CCL:About Artificial Intelligence X-Confirm-Reading-To: "Mr HG Kruger" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: <117D0A015B4@che.und.ac.za> Dear CCLers, I am trying to get background information on Artificial Intelligence. Review articles explaining a bit about the philosophy and principles as well as available software. I will summarise the answers. Many thanks Gert Kruger __________________________________________________________ Dr HG Kruger, Dept Chemistry, University of Natal, PO Box 18091, Dalbridge 4014, Durban, South Afica Tel +27-31-2602181 Fax +27-31-2603091 Email kruger@che.und.ac.za __________________________________________________________ From ccl@www.ccl.net Sat Feb 1 11:20:16 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA18369; Sat, 1 Feb 1997 10:47:54 -0500 (EST) Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by bedrock.ccl.net (8.8.3/950822.1) id KAA14625; Sat, 1 Feb 1997 10:47:52 -0500 (EST) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.8.3/8.8.0) with SMTP id XAA18609 for ; Sat, 1 Feb 1997 23:47:49 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA29990; Sun, 2 Feb 1997 02:19:17 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9702011546.AA09516@pack.crystal.uwa.edu.au> Subject: Mulliken Populations Summary To: CHEMISTRY@ccl.net Date: Sat, 1 Feb 97 23:45:59 WST Mailer: Elm [revision: 70.85] Dear All, Thank you so much for all who replied to my question regarding Mulliken Populations. Overall the conclusion seems to be that Mulliken Populations are very basis set depedent, thus what you put in is what you will get out. They should only be used as a 'rough' guide, for more accurate results different methods should be used, such as NBO and others. Regarding my problem, I am not interested in the exact popultion, I was only using it as a guide, but I was very surprised how Cadpac and G94 gave such different population analysis results even with the same basis set. Below are the responses. Thank you again. ************************************************************************** Original Question: Dear Computer Chemists, I have a question regarding Mulliken Populations, I appologise if this is an obvious question, but I haven't got much experience with mulliken populations, so I am not sure what is going on. How reliable are Mulliken Populations? The reason I ask is because, recently I ran two exactly the same jobs one using G94 and another using Cadpac and when I checked the charge distribution it was completely different. The final geometry and energies were the same, so I am confused. Also sometimes when I ran a job (water+metal) using G94 I get very strange charge distribution and other times it is as expected. Thank you for your time. Magda Wajrak *********************************************************************** Answer 1: Dear Magda, Mulliken Population analysis yield atomic charges that reflect mostly properties of the basis sets used rather than the actual distribution itself. Because of the MO description of Quantum Calculation, the molecule's electron density is divided into net popoulations and overlap populations. According to Mulliken's gross populations in the individual AO, the overlap population is equally divided between two AOs. In fact, there is no chemical ground for doing this. There have been suggested other definitions of charges : Bader charge : R.F.W. Bader, Atoms in molecules. A quantum theory (Clarendon Press, Oxford, 1990) Cioslowski's charge : J. Cioslowski, J. Am. Chem. Soc. 1989, 111, 8333. I hope it would help. Thanks, Cheol Ho Choi PhD Student Dept. of Chem. Georgetown Univ. Answer 2: It is known that the Mulliken population analysis is a breakdown for basis sets having diffuse functions [J. Baker, Theor.Chim.Acta, 68, 221(1985)]. Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-225-3724 e-mail: ep7@dent.okayama-u.ac.jp Answer 3: Douglas A. Smith asked: >The question: Can people please explain the concept of having a balanced >basis set and the dangers inherent in an unbalanced set? In particular, why >can I not simply use a large basis, including extra split valance functions, >polarization and diffuse functions, only on the atoms I need them on, and a >smaller, more compact basis set on the "unimportant" atoms to my chemical >question? This would certainly save time and resources during the calculation. In response, Per-Ola Norrby wrote: > I'll give it a try, and hopefully I can do it in chemists language >without loosing too much accuracy. > > The basic problem is that all basis sets are incomplete. There is >no way you can use a finite number of basis functions to describe the >electron density completely. You can get fairly close, but at a high cost. >Now, what happens to an atom with an incomplete basis? It has some >electron density that could be described better if it could use some >additional basis functions. Now, if there are unused basis functions on a >neighboring atom, there is always SOME way that a linear combination of >those can be used to stabilize the electron density on the original atom >further. Thus, the electron sharing between atoms is exaggerated and the >bonds look stronger than they actually are. This depends on how you determine the charge on each atom, and on how you determine bond strength. One must admit that adding more basis functions anywhere (lets ignore numerical presicion problems and near singular matricies for the moment) will give an improved approximation to the true (or HF) charge density. RFW Bader has shown us how to extract atomic charges and bond strengths (or bond orders) from the charge density. Using Baders definitions, these quantites (and many others) should improve as the approximation to the charge density improves. So one avoids the apparent paradox where augmenting the basis set decreases the quality of the answers you get. It should be no surprise that this works because Baders definitions of atomic charge and bond order are derived from the least action principle, as applied to a real physical quantity; the charge density. In fact Baders definitions, should really be called THE definitions. Things like Mulliken population analysis are hopelessly tied to the basis set, our approximation method for solving the SE. These numbers cannot possibly be considered "real physically observable quantities". If you modify your basis set, you can expect to get "funny" numbers >from the population analysis. This is just a demonstration that the numbers are meaningless, nothing else! > Now, if all atoms have very few basis functions, there aren't too >many unused functions that can be used by the neighbors, so the errors >(basis set deficiency and superposition errors, BSDE and BSSE) partially >cancel. However, if one atom has a very small basis set and the neighbor >many diffuse and polarization functions, you may get into a situation where >a very substantial part of the electron density of the first atom is >described by basis functions on the second. If you try to do a Mulliken >analysis on such a system, you get weird results. The electron density in >that region will also most probably be skewed, causing all kinds of >distortions. Yes exactly, but I interepret this as a definiciency in the polulation analysis method, rather than as a basis set problem. > You CAN get away with things like this, if you are careful to do >only comparisons between very similar systems, where the effect stays >constant. Naturally, you can get away with ANYTHING as long as you fulfill >that requirement :-) Or better yet, just ask physically meaningful questions of the wave function and charge density. > Per-Ola Norrby +--------------------------------------+-------------------------------------+ | Jan N. Reimers, Research Scientist | Sorry, Don't have time to write the | | Moli Energy (1990) Ltd. B.C. Canada | usual clever stuff in this spot. | | janr@molienergy.bc.ca | | +--------------------------------------+-------------------------------------+ Answer 5: Hi! It would seem tha there is an argument for relating charge distribution in a 'real' property. In the case of macro-molecular systems this can be done by aproximating point charges to reproduce the gradients or force constants produced by an scf. As the gradients and force constants can then be confirmed by comparason to experiment - this would seem a logical approach. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- Answer 6: Hi, there is another method of determining atomic charges, the NBO analysis of Reed, Weinhold and coworkers. The results quite independent of the basis set. Furthermore, the NBO analysis gives bond orders and the best Lewis stucture for the molecule. The NLMO part gives information on (hyper)conjugation. Review: Reed, Curtiss and Weinhold: JCP 1988, 88, p.899 Stefan __________________________________________________________ Stefan Fau, fau@mailer.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. D-35032 Marburg Answer 7: Hi, why does no one uses ( or is even aware of ) the population analysis method of Davidson, Roby, and Ahlrichs ? In my opinion, it is the cheapest one ( compared to Bader or NBO ) with the highest interpretation potential ( no one should use population charges to model the electrostatic potential of a molecule. These are quiet different things !!! ). Here are the references : (1) Ernest R. Davidson Electronic Population Analysis of Molecular Wavefunctions J. Chem. Phys. 46 (1967) 3320-3324 (2) Keith R. Roby Quantum theory of chemical valence concepts I. Definition of the charge on an atom in a molecule and of occupation numbers for electron density shared between atoms Mol. Phys. 27 (1974) 81-104 (3) Rolf Heinzmann and Reinhart Ahlrichs Population Analysis Based on Occupation Numbers of Modified Atomic Orbitals (MAOs) Theoret. Chim. Acta 42 (1976) 33-45 (4) D. W. J. Cruickshank, F.R.S., and Elizabeth J. Avramides The Interpretation of Molecular Wave Functions: The Development and Application of Roby's Method for Electron Population Analysis Phil. Trans. R. Soc. Lond. A 304 (1982) 533-565 (5) Claus Ehrhardt and Reinhart Ahlrichs Population analysis based on occupation numbers II. Relationship between shared electron numbers and bond energies and characterization of hypervalent contributions Theor. Chim. Acta 68 (1985) 231-245 Ciao, Heinz --- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com Answer 8: For a fairly systematic comparison of basis set and electron correlation dependence of Mulliken, APT, NBO, and CHELP charges, see: F. De Proft, J. M. L. Martin, and P. Geerlings, ``On the performance of density functional methods for describing atomic populations, dipole moments and infrared intensities'' Chemical Physics Letters 250, 393--401 (1996). In a nutshell, Mulliken has the most severe basis set dependence but the weakest correlation dependence, while the opposite is true for APT. Furthermore, B3LYP APT charges are in excellent agreement with QCISD ones with the same basis set. In effect, B3LYP APT charges with a basis set of at least split-valence plus polarization quality will be close to converged. Topological (Bader) charges are furthermore considered in P. Geerlings, F. De Proft, and J. M. L. Martin, ``Density-Functional Theory Concepts and Techniques for Studying Molecular Charge Distributions and Related Properties'', in Density-Functional methods in chemistry (eds. J. Seminario and P. Politzer), Elsevier, 1996 Sincerely, Jan M.L. Martin ---------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitfached k'lal ---- From toukie@zui.unizh.ch Mon Feb 3 08:20:39 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id IAA01625; Mon, 3 Feb 1997 08:01:40 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA01679; Tue, 4 Feb 1997 14:06:56 +0100 Message-Id: <1.5.4.32.19970203130306.0066fb20@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 03 Feb 1997 14:03:06 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOBOSOL and MOPAC50ESP Cc: toukie@zui.unizh.ch Dear Colleagues; I have bben looking for the two programmes MOBOSOL and MOPAC50ESP. I found FTP sites for them via Lycos, but I simply could not access the sites. Does anyone know from a publically-accessible site from which either or both of these programmes can be downloaded? Thanks, S. Shapiro toukie@zui.unizh.ch From qiecx@mluche5.chemie.uni-halle.de Tue Feb 4 05:20:50 1997 Received: from mluche5.chemie.uni-halle.de for qiecx@mluche5.chemie.uni-halle.de by www.ccl.net (8.8.3/950822.1) id EAA10877; Tue, 4 Feb 1997 04:57:38 -0500 (EST) Received: by mluche5.chemie.uni-halle.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id JAA10927; Tue, 4 Feb 1997 09:49:40 GMT From: "Anne Fircks" Message-Id: <9702041049.ZM10925@mluche5.chemie.uni-halle.de> Date: Tue, 4 Feb 1997 10:49:32 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: GROMOS 96 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Is anybody else using the new MD-package GROMOS 96 ? I would like to discuss some features of the program. For example, could somebody explain, why in the topology building blocks H-atoms are sometimes added to aromatic C-atoms and sometimes not? So in benzoic acid, but not in p-methylbenzyl-alcoholate or in PHE and TRP, but not in HIS and never in nucleotides ? Any help would be great Anne From joffre@cit.enscm.fr Tue Feb 4 06:20:50 1997 Received: from cit.enscm.fr for joffre@cit.enscm.fr by www.ccl.net (8.8.3/950822.1) id GAA11201; Tue, 4 Feb 1997 06:03:39 -0500 (EST) Received: from [193.52.205.115] by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA10180; Tue, 4 Feb 1997 12:00:47 +0100 Message-Id: <32F7172E.576E@cit.enscm.fr> Date: Tue, 04 Feb 1997 12:02:06 +0100 From: Jacques JOFFRE Reply-To: joffre@cit.enscm.fr Organization: Ecole de Chimie de Montpellier UMR 5618 X-Mailer: Mozilla 3.0Gold (Win95; I) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Uranium and G94W Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL users, We are trying to compute the UO2++ cation with G94 for Windows (RevB.2). For Uranium we use the ECP of Hay (J. Chem. Phys. 71, 1767, 1979) but we get an error message "Unable to normalize a contracted basis function". However, a friend of mine, ran the job on a SG unix workstation and a G94 D release, without problem. We sent 4 e-mails to gaussian without any reply. Any advice from G94W users will be welcome. This is the failing file : rhf/gen pseudo=cards test gfprint U 2 1 U O1 U 1.72 O2 U 1.72 O1 180.0 O 0 STO-3G **** U 0 s 4 1.00 1.7510 -2.55661 0.0 0.9817 2.89155 0.0 0.3430 1.0 0.0 0.1200 1.0 0.0 p 4 1.00 2.8030 -0.23065 0.0 0.6507 1.10576 0.0 0.2668 1.0 0.0 0.1200 1.0 0.0 d 3 1.00 4.9630 -0.02952 0.0 0.5652 1.00469 0.0 0.1904 1.0 0.0 f 4 1.00 9.9320 0.09411 0.0 3.3360 0.43691 0.0 1.1650 0.65431 0.0 0.3655 1.0 0.0 **** U 0 ECP-U 4 78 projection g et superieur 7 0 14.1854 -0.225271 1 353.9256 51.945269 2 113.3707 -505.522542 2 31.0962 -203.335259 2 10.7324 -67.533267 2 3.6015 -22.930558 2 1.3043 -1.713933 projection sg 8 0 173.4721 0.870627 1 664.8590 67.456969 2 197.7844 958.648409 2 65.8127 572.524468 2 18.7086 52.135348 2 8.3551 122.079158 2 3.0358 39.809700 2 1.1031 5.174945 projection pg 7 0 336.4847 1.841438 1 259.5891 47.861892 2 98.5246 692.999403 2 15.3957 71.453617 2 9.5292 165.434882 2 3.2468 49.231836 2 1.0757 6.205529 projection dg 7 0 113.9900 2.908206 1 138.0140 34.232320 2 31.3510 96.247682 2 19.9354 314.298307 2 7.5077 127.384204 2 2.4365 33.925873 2 0.6817 3.290444 projection fg 9 0 45.3127 3.935033 1 3585.7634 259.780179 2 856.9634 4358.700266 2 190.6303 926.650196 2 41.8509 255.708045 2 12.8356 81.482914 2 3.7764 14.932765 2 0.8058 -0.661727 2 0.2811 -0.158290 -- Jacques JOFFRE joffre@cit.enscm.fr Laboratoire de Materiaux Catalytiques UMR ENSCM/CNRS 5618 Ecole Nationale Superieure de Chimie 8, rue Ecole Normale Tel : 04 67 14 72 47 34053 Montpellier + 04 67 14 43 26 ---------------------------------------------- From campagne@incm.u-nancy.fr Tue Feb 4 06:23:04 1997 Received: from brown.incm.u-nancy.fr for campagne@incm.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id GAA11236; Tue, 4 Feb 1997 06:12:02 -0500 (EST) Received: from yellow.incm.u-nancy.fr by brown.incm.u-nancy.fr via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@brown.incm.u-nancy.fr:chemistry@www.ccl.net> id MAA29930; Tue, 4 Feb 1997 12:15:11 GMT Received: from yellow.incm.u-nancy.fr (localhost [127.0.0.1]) by yellow.incm.u-nancy.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA08864 for ; Tue, 4 Feb 1997 12:15:09 GMT Sender: campagne@incm.u-nancy.fr Message-ID: <32F7284C.1CFB@incm.u-nancy.fr> Date: Tue, 04 Feb 1997 12:15:08 +0000 From: Fabien Campagne Organization: Laboratoire de Chimie The'orique de Nancy X-Mailer: Mozilla 3.0SC-SGI (X11; I; IRIX64 6.2 IP28) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL: Viseur: a GPCR visualization program. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers: I would like to announce here the release of the Viseur program version 3.0. Viseur is a program that let you manage and visualize your preferred GPCRs (G Protein-Coupled Receptors: a membrane receptor superfamily). The program, running on SGI workstations, and distributed free of charge for academics was developed in collaboration with Sanofi Recherche Montpellier, a subsidiary of the Elf Sanofi group. Viseur provides the user with valuable features : - SwissProt, MSF, PDB file format support - Sequence visualization - Snake-like visualization - Alignment visualization and edition - 3D Model visualization - Interaction with the TinyGRAP mutant database (new in 3.0 release) - PostScript and EPS outputs - Painting module to highlight residue common properties (used to higlight residues that were mutated according to the TinyGRAP information) - HTML (snake-like) and VRML (3D Model) outputs for Web publishing of annotated receptors The Viseur program is intended to be used to assist in GPCR modeling. The program will let you build manually sequence alignments, look at the same time at helix limits (snake-like view), and change these limits interactively. Raw 3D Models can be constructed immediately to evaluate the result of changes in the alignment. For more information about the program features, program distribution, and more, please visit: http://brown.incm.u-nancy.fr/viseur/viseur.html (Viseur Home page) http://brown.incm.u-nancy.fr/viseur/using/documentation/main.html (Documentation main page) http://brown.incm.u-nancy.fr/viseur/snake-like-view/OPRD_HUMAN.html (snake-like clickable HTML output illustration) http://brown.incm.u-nancy.fr/viseur/BACTER_RHODO.wrl.gz (3DModel VRML output illustration) http://brown.incm.u-nancy.fr/viseur/using/documentation/ViseurTinyGRAP.html (TinyGRAP mutants visualization) best regards, Fabien Campagne -- campagne@incm.u-nancy.fr | Lab. de Chimie Theorique phone: (033) 83 91 20 00 extension 3236 | Nancy, France. From Vincent@averell.umh.ac.be Tue Feb 4 08:20:54 1997 Received: from averell.umh.ac.be for Vincent@averell.umh.ac.be by www.ccl.net (8.8.3/950822.1) id HAA11690; Tue, 4 Feb 1997 07:40:11 -0500 (EST) From: Received: by averell.umh.ac.be (AIX 3.2/UCB 5.64/4.03) id AA29342; Tue, 4 Feb 1997 13:26:02 +0100 Message-Id: <9702041226.AA29342@averell.umh.ac.be> Subject: Rb and K 6-31G** basis set requested To: chemistry@www.ccl.net (CCL-request) Date: Tue, 4 Feb 1997 13:26:02 +0100 (NFT) X-Mailer: ELM [version 2.4 PL0] Content-Type: text Hello Everybody, I need to perfom calculation on Rubidium and Potassium species, using Gaussian 94. However it seems that 6-31 G** basis sets are missing for those elements. So could somebody help me to find those basis sets for Rb and K (references, web sites or basis sets themselves). Thank you very much for your help. Vincent **************************************************************** * Vincent Parente * * Service de Chimie des Materiaux Nouveaux * * Center for Research in Molecular Electronics and Photonics * * University of Mons-Hainaut * * 20, Place du Parc, B-7000 Mons, BELGIUM * * tel : +32 65 37 3361 * * fax : +32 65 37 3366 * * +32 65 37 3054 * * e-mail : Vincent@averell.umh.ac.be * * http://morris.umh.ac.be/ * * http://morris.umh.ac.be/Vincent/vince.htm * **************************************************************** From SUTJIANTO@axp.cmt.anl.gov Tue Feb 4 10:20:53 1997 Received: from axp.cmt.anl.gov for SUTJIANTO@axp.cmt.anl.gov by www.ccl.net (8.8.3/950822.1) id JAA12360; Tue, 4 Feb 1997 09:24:43 -0500 (EST) Date: Tue, 4 Feb 1997 8:24:46 -0600 From: Amin Sutjianto Reply-To: SUTJIANTO@cmt.anl.gov To: CHEMISTRY@www.ccl.net Message-Id: <970204082446.22e08abc@axp.cmt.anl.gov> Subject: g94: charge and massage options Dear All, Could anybody tell me whether there is any different between "charge" and "massage" options in G94? For example, if I want to define a point charge at certain position near a molecule, should we expect the same result (in total energy) for both options? Thank you much. Amin From perlstein@chem.chem.rochester.edu Tue Feb 4 12:20:55 1997 Received: from chem.chem.rochester.edu for perlstein@chem.chem.rochester.edu by www.ccl.net (8.8.3/950822.1) id LAA13264; Tue, 4 Feb 1997 11:32:23 -0500 (EST) Received: from stc (stc.chem.rochester.edu [128.151.176.25]) by chem.chem.rochester.edu (8.8.4/8.8.4) with SMTP id LAA01348; Tue, 4 Feb 1997 11:31:47 -0500 (EST) Message-ID: <32F79005.4D94@chem.chem.rochester.edu> Date: Tue, 04 Feb 1997 11:37:41 -0800 From: jerry perlstein Organization: university of rochester X-Mailer: Mozilla 3.0C-nnie30 (Win16; U) MIME-Version: 1.0 To: "Douglas A. Smith Ph.D." CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:crystal packing calculations and programs References: <199702011452.JAA19298@home.CTCnet.Net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Leslie Glasser gave some references to crystal packing in response to Doug Smith's query, to which I would add the following additional references: A. Gavezzotti and G. Filippini JACS 118, 7153 (1996) A. M. Chaka et al. Acta Cryst. B52, 165 (1996) B. B. P. van Eijck et al. Acta Cryst. B51, 99 (1995) J. Perlstein, JACS 116, 11420 (1994) A. Gavezzotti, Acc. Chem. Res 27, 309, (1994) W. Linert and F. Renz J. Chem. Inf. Comput. Sci. 33, 776 (1993) H. R. Karfunkel and F.J.J. Leusen Speedup Journal 6, 43,(1992) good luck finding this one, but it's quite good. Douglas A. Smith also wrote: > > > What are the options when one does not have the crystal structure available? > Can one reasonably start from a high quality ab initio calculation on a > single molecule (gas phase) and use that structure to pack a crystal? Generally no. The gas phase strucuture will be a local minimum but not necessarily the minimum seen in the crystal structure. You need only look at molecules which crystallize in different polymorphs to convince yourself of this. See A. Gavezzotti and G. Filippini, JACS 117, 12299 (1995) for a long list of these. Also as pointed out by Leslie, even if you get the correct molecular local minimum to start with, you still don't know the space group to use. Again since organic crystals are polymorphic, there will usually be more than one space group. > > What packages are out there, commercial and "public domain" (free, QCPE, > etc.) that can perform crystal packing calculations? There are a number of packages; in no particular order: 1)PCK83 QCPE program no. 481 by D. J. Williams and also sold commerically by Williams 2)C2-POLYMORPH by Leusen and Karfunkel. A module for the Cerius2 molecular modeling package from MSI 3)PACK by J. Perlstein, a module for the CHEMX/CHEMLIB molecular modeling package from Chemical Design, Inc. 4)PROMET by A. Gavezzotti None of the packages are capable of predicting space groups and most of them cannot handle more than 1 or 2 single bond rotations. (PACK can handle about 12 for monolayer crystal structures. If you get the monolayer correctly, you can get the rest of the crystal packing.) -- ************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627-0216 Tel: (716)275-2511 FAX: (716)242-9485 perlstein@chem.chem.rochester.edu http://stcoff.chem.rochester.edu/perlstein.html From marti108@gold.tc.umn.edu Tue Feb 4 15:20:55 1997 Received: from mhub1.tc.umn.edu for marti108@gold.tc.umn.edu by www.ccl.net (8.8.3/950822.1) id OAA14943; Tue, 4 Feb 1997 14:41:26 -0500 (EST) Received: from gold.tc.umn.edu by mhub1.tc.umn.edu; Tue, 4 Feb 97 13:41:27 -0600 Received: by gold.tc.umn.edu; Tue, 4 Feb 97 13:41:26 -0600 Date: Tue, 4 Feb 1997 13:41:25 -0600 (CST) From: Marcus G Martin To: chemistry@www.ccl.net Subject: Modeling Electrostatics - summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is the summary of useful responses to my question about fitting an electrostatic potential. The general feeling appears to be that population analysis is not the way to do this. my original question What should I do if I want to fit the electrostatic potential of a molecule? I have been fitting lennard-jones 12-6 force fields to alkanes and would like to move into the (frightening) world of slightly charged molecules. Nothing extremely painful, such as water, but more like alkanols or carboxyllic acids. The running discussion on charges appears to me to say that the charges computed from quantum mechanics are of little use for fitting a force field. I would like to know if the computational community has a feel for what the 'best' and most efficient way of fitting point charges to these molecules would be. thanks, I will summarize the responses if there is interest. [1] reply From: Konrad Hinsen T > The running discussion on charges appears to me to say that the > charges computed from quantum mechanics are of little use for fitting a > force field. I would like to know if the computational community has a Right. > feel for what the 'best' and most efficient way of fitting point charges > to these molecules would be. There has been a long discussion about this topic a while ago; you should find it in the archives. Basically, you fit the charges to reproduce the electrostatic potential at a certain distance from the molecule (more or less where you would find the atoms of the neighbouring molecules). Personally, I consider it essential to use an SVD-based fitting techniques, since otherwise you will suffer from instabilities (see any textbook on least-squares problems for an explanation). I haven't found anyone openly disagreeing with this statement, but on the other hand almost no one uses SVD-based methods, because the standard programs don't offer them. Konrad Hinsen | E-Mail:hinsen@ibs.ibs.fr---------------------------------------------------- Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais [2] reply From: Shawn Huston Fit your point charges to an an obervable for the environment you expect the model to mimic. For example,if you need to represent the (polarized) charge distribution a moleculewill exhibit in a polar medium (such as water) then you want a set of point charges that yields at least the molecular dipole moment in water. Details can be found in many papers by W. Jorgensen (look at the early ones from the 80's where you will find more information). Shawn Shawn Huston Sr. Marketing Scientist (don't forget the trailing 'h' in my email alias: shawnh@mdli.com) MDL Information Systems Phone: 510-895-1313 X 1145 14600 Catalina Street Fax: 510-483-4738 San Leandro, CA 94577 http://www.mdli.com [3] reply From:dew01@xray5.chem.louisville.edu(Donald E. Williams) Hi, You may be interested in my paper which appeared in J. Comp. Chem. 1994, 15, 719. The MEP of n-alkanes is not well represented by net atomic charges. Additional charge sites at methylene bisector locations allow a good fit. Also, I recently announced the software pdm97 on ccl, which fits site multipole models to the MEP. I assume that you got that, but if you didn't, let me know and I will send it directly to you. -Donald Williams dew01@xray5.chem.louisville.edu [4] reply From: "Dr. Heinz Schiffer" Hi Marcus, I think there is a misunderstanding. There are no such things like charges of atoms in a molecule in quantum mechanics. They are not observables. Every partitioning of the charge density of a molecule into atomic ( or other ) subunits are completely arbitrary ! O.k. this is a little bit overdone. The population analysis of a molecular wavefunction is only useful for interpretation purposes, like : which atom is more negatively charged and is likely to be attacked by an electrophile an so on... The electrostatic potential of a molecule on the other hand is an observable and rigorously defined in quantum mechanics. This potential can be calculated point wise in the space around a molecule with most ab intio and also with some semi-empirical programs. This potential can than be modelled by a point charge model of a molecule, that is you adjust the charges of the model so, that the potential calculated with these charges is (nearly) the same as the ab initio calculated one. There exist many schemes around for fitting charges to the electrostatic potential, but they all try to model the electrostatic potential of the molecule. Population anlysis charges are never meant to modell the electrostatic potential of a molecule, they serve "only" for interpretation purposes of a molecular wave-function. The best way to get charges for your purpose is to fit them to the electrostatic potential. Hope this helps, Ciao Heinz Dr. Heinz Schiffer Phone ++49-69-305-2330-- Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From XIENING@MEENA.CC.UREGINA.CA Tue Feb 4 16:20:57 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id QAA15906; Tue, 4 Feb 1997 16:19:43 -0500 (EST) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-6 #20153) id <01IF0TSRIJ469PM4PL@meena.cc.uregina.ca> for chemistry@www.ccl.net; Tue, 4 Feb 1997 15:19:37 CST Date: Tue, 04 Feb 1997 15:19:36 -0600 (CST) From: "Xie, Ning" Subject: HOMO & LUMO energies of MnO4- To: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hi, there, Is there anybody who'd like to share his expertise in calculating the MO energies of MnO4- (permanganate ion) with us? I tried semi-emperical method with basis set ZINDO/1 but the result is not satisfied. I tried ab initio method using G94w, it gave error massages. Any information is appreciated. Thank you. ========================================================================= | XIE, NING Tel: (306)585-5262 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina E-Mail: xiening@meena.cc.uregina.ca | | Regina, SK or: xiening2@max.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= From hxt10@po.cwru.edu Tue Feb 4 17:20:57 1997 Received: from babar.INS.CWRU.Edu for hxt10@po.cwru.edu by www.ccl.net (8.8.3/950822.1) id QAA16067; Tue, 4 Feb 1997 16:51:59 -0500 (EST) Received: from hxt10-ra.cwru.edu (dialin059.REMOTE.CWRU.Edu [129.22.220.59]) by babar.INS.CWRU.Edu with ESMTP (8.7.6+cwru/CWRU-3.0) id QAA04617; Tue, 4 Feb 1997 16:52:00 -0500 (EST) (from hxt10@po.cwru.edu for ) Message-Id: <199702042152.QAA04617@babar.INS.CWRU.Edu> From: "Hui-Hsu (Gavin) Tsai" To: Subject: normal modes program Date: Tue, 4 Feb 1997 16:52:32 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCLers: Could anybody tell me what program can show the vibration normal modes >from Gaussian output files? Thanks a lot! Hui-Hsu (Gavin) Tsai Ph.D. student in the Chemistry Department Case Western Reserve University E-mail : hxt10@po.cwru.edu Tel : (O)(216)368-3730 (H)(216)229-5913