From RICHM@ACFcluster.NYU.EDU Mon Sep 19 20:07:02 1994 Received: from acf6.acf.nyu.edu for RICHM@ACFcluster.NYU.EDU by www.ccl.net (8.6.9/930601.1506) id TAA21558; Mon, 19 Sep 1994 19:02:42 -0400 From: Received: from ACFcluster.NYU.EDU by ACFcluster.NYU.EDU (PMDF V4.3-8 #8043) id <01HHB2A1IMDOSW31IH@ACFcluster.NYU.EDU>; Mon, 19 Sep 1994 19:03:18 EDT Date: Mon, 19 Sep 1994 19:03:18 -0400 (EDT) Subject: CCL:CompChem in High Schools To: chemistry@ccl.net Message-id: <01HHB2A1IW1ASW31IH@ACFcluster.NYU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT In response to Robert Gotwals posting about computational chemistry at the high school level, I would like to bring to the attention of the group a site specifically aimed at introducing molecular modeling to high school students. In fact,the original modules we are presently developing are being tested on 9th grade physical science students. We find that software available over the net (MAGE, Raswin and XMol) are excellent for student activities. When time permits please take a look at the site. We would appreicate any and all suggestions. MATHMOL --K-12 Mathematics and Molecules http://www.nyu.edu/docs/providers/rich/education/mathmol/mathmol.html Marv Rich From mulcrone@luigistoaster.pds.charlotte.nc.us Tue Sep 20 07:58:57 1994 Received: from luigistoaster.pds.charlotte.nc.us for mulcrone@luigistoaster.pds.charlotte.nc.us by www.ccl.net (8.6.9/930601.1506) id HAA28506; Tue, 20 Sep 1994 07:37:13 -0400 Received: by luigistoaster.pds.charlotte.nc.us (5.65/DEC-Ultrix/4.3) id AA06154; Tue, 20 Sep 1994 07:37:14 -0400 Date: Tue, 20 Sep 1994 07:37:14 -0400 From: mulcrone@luigistoaster.pds.charlotte.nc.us (Daniel Mulcrone) Message-Id: <9409201137.AA06154@luigistoaster.pds.charlotte.nc.us> To: CHEMISTRY@ccl.net Subject: scandium Hello all-- I am a tenth grade student at Providence Day School in Charlotte, North Carolina. In our chemistry class, we were assigned a paper on "our favorite element." I was given the element Scandium. There is a length requirement of three pages for this report. I am having some trouble finding enough info on Scandium to fill three pages. My chemistry teacher told me that Scandium is used in the Airline industry. How? If anyone has any information about this element, please mail me. Any help would be greatly appreciated. Thanks in advance! mulcrone@luigistoaster.pds.charlotte.nc.us From szilagyi@indy.mars.vein.hu Tue Sep 20 08:03:38 1994 Received: from sztaki.hu for szilagyi@indy.mars.vein.hu by www.ccl.net (8.6.9/930601.1506) id HAA28433; Tue, 20 Sep 1994 07:22:32 -0400 Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id Od01781; Tue, 20 Sep 1994 13:21:54 +0200 Received: by miat0.vein.hu with SMTP (5.61++/Vein-1.0) id AA04829; Tue, 20 Sep 94 13:24:59 +0200 Received: by indy.mars.vein.hu (931110.SGI/930416.SGI.AUTO) for @miat0.vein.hu:ben016@almos.vein.hu id AA00865; Tue, 20 Sep 94 13:24:38 +0200 From: "Robert K. Szilagyi" Message-Id: <9409201324.ZM863@indy.mars.vein.hu> Date: Tue, 20 Sep 1994 13:24:31 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net, ben016@almos.vein.hu Subject: Summary of Steric Effect Calculation Cc: szilagyi@indy.mars.vein.hu Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Charset: US X-Char-Esc: 0 Dear Comp.-Chem.-List, a couple of weeks ago I posted a message about calculation and/or QUANTITATIVE prediction of steric effect. I received many valuable comments and hints concerning this topic. Thanks for everyone, who made any contribution. Here comes the summary: ************************* CUT HERE ! *********************************** -------------------------+---------------------------------------------- topper@magnum.cooper.edu | Robert Topper -------------------------+---------------------------------------------- You may be interested in a series of articles by D.F. DeTar in recent issues of the Journal of Organic Chemistry. ------------------------------+----------------------------------------- >From STEWARTK@cmda.abbott.com | Kent Stewart ------------------------------+----------------------------------------- For information regarding steric effects within organic compounds, here are two refereces: 1. "Substituent Constants for Correlation Analysis in Chemistry and Biology" Hansch, C. and Leo, A., book published by John Wiley, See chapter 2. 2. White, D. et al., J. Compu. Chem. 14, 1042-1049 (1993) -------------------------------+---------------------------------------- >From jas@medinah.atc.ucarb.com | Jack -------------------------------+---------------------------------------- The most common measure of bulkiness I've seen is the Tolman Cone Angle, primarily used for symmetric phosphines, but quite adaptable to other (including non-symmetric) ligands. I've observed an interesting correlation, however, between the cone angle (as well as other measures of size) and the ratio of volume to surface area (V/SA) as determined from isodensity surfaces (roughly the vDW surface). For a sphere this would just be related to the radius, but for conical shapes it varies with both cone angle and extent. What I like about V/SA is that it's independent of a reference point and removes the arbitrariness about contact points (no need to "fold" everything back into a cone shape). It's also relatively insensitive to torsional degrees of freedom. It's not clear, though, whether "extent" is relevant as cone angle. Perhaps some normalization scheme (based on principle axes/moments, e.g.) could be used to remove (or deemphasize) the "extendedness". [By the way, if you run across anything published along these lines, I'd appreciate the reference. In any case, if you (or anyone else reading this) find V/SA to be a useful measure of steric size/bulk, I'd appreciate a note.] Ted Brown (at Northwestern, I believe) does a MM-based substrate docking "experiment" to quantify the steric effects (repulsive force) of ligands (bound to a metal carbonyl complex, if I recall correctly). --------------------------------+--------------------------------------- WSTEINMETZ@POMONA.claremont.edu | Wayne E. Steinmetz --------------------------------+--------------------------------------- May I suggest CoMFA (Comparative Molecular Field Analysis) as a vehicle to correlate reactivity with steric effects. The technique is described in detail in H. Kubinyi, Ed., 3D QSAR in Drug Design, ESCOM, Leiden, 1993. CoMFA was originally developed by medicinal chemists but can also be applied to problems from organic and inorganic chemistry. In applying the technique, one completes the following steps: 1) calculate structures and partial charges via MOPAC or AMPAC of the molecules in the dataset 2) superimpose the molecules in the dataset, 3) imbed the superimposed molecules in a lattice with a lattice spacing of 1 to 2 Angstrom, 4) calculate at each lattice position the interaction energy of a probe molecule with each molecule in the dataset, 5) correlate the chemical property with the interaction energies using the method of partial least squares. The method was developed by Richard Cramer of Tripos Associates and is part of the Sybyl software package. I recently submitted an article to Inorganic Chemistry in which I showed that CoMFA can handle the steric effects of ligands in a range of inorganic reactions. ------------------------+----------------------------------------------- gford@sgi1.chem.smu.edu | George ------------------------+----------------------------------------------- A good starting point would probably be Taft's steric parameters (Es). These are derived directly from experimental rate data (acid and base hydrolysis of carboxylate esters) and do not therefore depend on rather poorly defined notions of van der Waals radii, surfaces, volues, etc. You can find compilations of Es parameters in virtually any book on physical organic chemistry. For a particularly complete compilation see for example: "A critical compilation of substituent constants" by Otto Exner in: "Correlation Analysis in Chemistry", N.B. Chapman and J. Shorter, Plenum, Press, 1978, pp. 439-540. -----------------------+------------------------------------------------ MARTIN@cmda.abbott.com | -----------------------+------------------------------------------------ Look up Marvin Charton's work. Some old references I have: (1) Charton, M. "The Upsilon Steric Parameter -- Definition and Determination," In Topics in Current Chemistry; (Vol.114 of ; M. Charton and I. Motoc, Ed.; Springer-Verlag: Berlin, 1983; pp 57-91. (2) Charton, M. "Volume and Bulk Parameters," In Topics in Current Chemistry; (Vol.114 of Topics in Current Chemistry) ; M. Charton and I. Motoc, Ed.; (F. L. Bosche, Series Ed.) Springer-Verlag: Berlin, 1983; pp 107-118. (3) Charton, M.; Motoc, I., Ed.; Steric Effects in Drug Design; Springer-Verlag: Berlin, 1983; Vol. 114. ----------------------------------+------------------------------------- dwhite@assistant.beckman.uiuc.edu | Dave ----------------------------------+------------------------------------- There are two recent reviews in this area: White, D and Coville, N.J. Advances in Organometallic Chemistry, 36 (1994) 95 Brown, T.L. and Lee, K.J. Coord. Chem. Rev. 128 (1993) 89. Basically there are three different methodologies to choose from: cone angles (Tolman, chem. rev. 77 (1977) 313), solid angles (White et al., J. Comput. Chem. 14 (1993) 1042) and ligand repulsive energies (Brown, Inorg. Chem. 31 (1992) 1286). There are some other measures used in Organic chemistry and they are tabulated and referenced in the Advances in Organomet. Chem review. Ted Brown and myself are going to be generating ligand repulsive energy values for alkyl and other organic based groups in the near future. If you have specific values which you require please send them to me and I shall include them in the lsit of values to be generated. --------------------------+--------------------------------------------- yurel@stamail1.vut.edu.au | --------------------------+--------------------------------------------- I'm studing the steric effects of ammine ligands and will be very interested in responses you get. There were few studies involving the quantification of steric ligand factors. Earlier Tolman [1] introduced CONE ANGLE values calculated with the use of simple CPK models for the comparison of the steric properties of monodentate tertiary phosphine ligands. Recently, Brown [2] utilised LIGAND REPULSIVE ENERGY as the measure of ligand steric features based on molecular mechanics calculations. 1. C.A. Tolman, Chemical Reviews, 77 (1977) 313. 2. T.L.Brown, Inorg. Chem., 31 (1992) 1286. ************************* END OF THE SUMMARY **************************** If I receive further responses I will update the previous summary, of course. Cheers, Rob -- ----------------------------------------------------------------------------- Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 ----------------------------------------------------------------------------- From mercie@mail.med.cornell.edu Tue Sep 20 11:59:00 1994 Received: from mail.med.cornell.edu for mercie@mail.med.cornell.edu by www.ccl.net (8.6.9/930601.1506) id LAA04029; Tue, 20 Sep 1994 11:33:29 -0400 Received: (from mercie@localhost) by mail.med.cornell.edu (8.6.9/ech1.75) id LAA23701; Tue, 20 Sep 1994 11:33:27 -0400 Date: Tue, 20 Sep 1994 11:33:26 -0400 (EDT) From: Gustavo Mercier To: Amin Sutjianto cc: CHEMISTRY@ccl.net Subject: Re: CCL:Durand-Barthelat's ECP In-Reply-To: <940917101236.20219a9d@cmt.anl.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 17 Sep 1994, Amin Sutjianto wrote: > > Hi Netters, > > I would like to know whether Durand-Barthelat's effective core pseudo- > potential basis set can be used in GAUSSIAN90. I would appreciate > very much if you could tell me how to prepare the input file. > Hi! If this effective core pseudopotential is of the same form as the one in G.B. Bachelet et. al. Physical Rev. B. v. 26, no.8 1982, p. 4199, then the form is different from the one used in the Gaussian Programs. You may try instead the pseudopotentials from Krauss et. al.. See info below. The following references should provide you with very recent ECP's for most of the periodic table. The comments I have heard from those who have used them are rather favorable (comments limited to energetics and geometries, but recent work on spectroscopy by Garmer and Krauss is rather impressive): Stevens et. al. J. Chem.Phys. 81 (12), Pt. II, 1984 First and Second Row atoms Stevens et. al. Can. J. Chem. 70, 612, (1992) Third through Fifth row atoms. Some typos are known: Table 2: In RECP for second Vp-f component: -129.87594 should read -129.78594 Table 4: Basis for Fe Cp term for 1sp should be -0.007940, not -0.07940 asp term for 4sp should be 0.0410, not 0.410 Table 7: Result for Be Eval with core a should read -1.01214, not -0.01214 Cundari and Stevens J. Chem. Phys. 98 (7) 1993 Lanthanides I hope this is useful. These papers also discuss the variety of methods available to generate ECP's, relativistic effects and references to ECP's for DFT computations. Good Luck Gustavo A. Mercier, Jr. mercie@cumc.cornell.edu From jan@vodka.chem.TU-Berlin.DE Tue Sep 20 13:59:03 1994 Received: from vodka.chem.TU-Berlin.DE for jan@vodka.chem.TU-Berlin.DE by www.ccl.net (8.6.9/930601.1506) id NAA05930; Tue, 20 Sep 1994 13:23:40 -0400 Received: by vodka.chem.TU-Berlin.DE (AIX 3.2/UCB 5.64/4.03) id AA19334; Tue, 20 Sep 1994 19:18:50 +0100 Date: Tue, 20 Sep 1994 19:18:50 +0100 From: jan@vodka.chem.TU-Berlin.DE (Jan Hrusak) Message-Id: <9409201818.AA19334@vodka.chem.TU-Berlin.DE> To: CHEMISTRY@ccl.net Subject: Durand-Barthelat's ECP Cc: SUTJIANTO@cmt.anl.gov On Sat, 17 Sep 1994, Amin Sutjianto wrote: > > Hi Netters, > > I would like to know whether Durand-Barthelat's effective core pseudo- > potential basis set can be used in GAUSSIAN90. I would appreciate > very much if you could tell me how to prepare the input file. > HI The Durand-Barthelat's ECP can be used in the GAUSSIANxx code, since the analytical form is the same as for the Kraus, Stevens, Stoll etc. However, in the ECP routine of GAUSSIANxx are (contrary to GAMESS or MOLPRO) some restrictions according to the power of (r) in the ECP expression and so one has to check if the ECP parameters are read properly. For some higher powers the program replace the (n) by 0. You have also to read the Handbook for the correct handling of the Jacobi term in the ECP. Jan Hrusak jan@vodka.chem.tu-berlin.de From u45617@uicvm.uic.edu Tue Sep 20 14:02:50 1994 Received: from UICVM.UIC.EDU for u45617@uicvm.uic.edu by www.ccl.net (8.6.9/930601.1506) id NAA06659; Tue, 20 Sep 1994 13:45:06 -0400 Date: Tue, 20 Sep 1994 13:45:06 -0400 Message-Id: <199409201745.NAA06659@www.ccl.net> Received: from [128.248.78.161] by UICVM.UIC.EDU (IBM VM SMTP V2R2) with TCP; Tue, 20 Sep 94 12:41:07 CDT X-Sender: u45617@uicvm.uic.edu (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: u45617@uicvm.uic.edu (Hopfinger at UICVM) Subject: Validation of Modeling Software Validation of Modeling Software 1. Background With the current high level of interest in molecular modeling, increasingly sophisticated software is being offered by over 200 commercial organizations in the US. and Europe. This software can be quite expensive and often requires advanced computer platforms for its successful use. Above all however, it is complicated. A typical modeling package may contain some ten program areas, each of which has numerous working levels and at each level there may be many commands, each of which offers many options to the user. Overall such a package may therefore have hundreds, or even thousands of commands and as a practical matter, users often restrict their activities to one or two specific program areas. They have less interest and little experience with the other available areas, but in the areas with which they work, they gain considerable experience and soon become experts in the particular subject. The accuracy, or validity of the results that can be developed by modeling programs is usually weighed by experts who use an informal process of external validation, i.e. comparing new result to results obtained in some other way. This may be merely use of an earlier version of the program or some truly external method, such as x-ray crystallography. Except for work done by individual users of the software, systematic efforts to provide external validation of modeling software have not been widespread. Validation carried out by individual users has a number of disadvantages. It tends to be focused upon the specific problem of interest, and is usually not published widely. More seriously, it can be significantly time-consuming. A small informal poll that we carried out in May/June, 1994 suggested that molecular modeling groups spend from person-months to well over a person-year working on the validation of new versions of familiar modeling software. This is wasteful of highly trained resources and moreover, because it has a narrow base, it is a validation scheme with little robustness. We propose here a more broadly based validation scheme, which will cover many of the competing computer programs and which, ideally, will be carried out by an independent group, which can retain an objective approach to the problem. Much in this proposal requires final definition and the proposal as a whole must be acceptable to the community if it is to succeed. For these reasons, a meeting to discuss the issues is being held in Baltimore in November, 1994. All interested parties are invited to attend and conclusions arrived at by consensus will be published in early 1995 in the Journal of Chemical Information and Computer Sciences. The purpose of this message is to present a tentative agenda for this meeting and to invite you to attend. If you feel your organization or company has been overlooked in this draft agenda, please contact us to be included in the endeavor. 2. Problems to be addressed Molecular modeling consists of a relatively large number of operations, many of which have their own character and corresponding software. It is not realistic to attempt to cover all components of molecular modeling in a first-pass analysis of validation of modeling software. Rather, acknowledging the breadth of the undertaking, and focusing on the current major molecular modeling components and tasks seems the best strategy to pursue. One working list of priority validation topics is, * Molecular mechanics - force fields and parameters * Statistical methods - QSAR/QSPR, data analysis * Conformational analysis * Docking and intermolecular Interactions * Molecular similarity analysis * Environmental / solvation methods * Molecular dynamics 3. Other Issues Very little is known about the process of validation of molecular modeling systems, and a minimalist approach seems best. The criteria laid out above represent a small first step towards a systematic validation effort. Determination and comparison of the structures of small flexible and rigid molecules are the most common of modeling tasks and offer themselves as a basis for validation. Still, one must be cognizant of the growing variety of applications of molecular modeling, and the corresponding added dimensions they bring to the validation problem. There is a need to identify what validation goals are common to all molecular modeling applications, and what goals are specific, but also central, to particular applications. For example, polymer molecular modeling will have different specific end-points than those of small-molecule drug design. Ab initio and semi-empirical calculations are not considered in this iteration. The entire issue of validation of such calculations, is a difficult issue, separate from that of dealing with molecular mechanics and molecular dynamics. 4. Acceptance of Standards Software developers are as aware as any one of the need for standards and of the role that validation could play in this area. They are sensitive however to cost-benefit considerations and any process that is too onerous (read: costly) will be adopted only with reluctance. This is another reason for a minimalist approach. If the modeling community has an agreed-upon and promulgated list of structures which can be used in validation, then individual vendors can work on members of this list, publishing their results, or not. The marketplace will respond to this and the vendors who made the correct choice will be rewarded. In this scenario, validation will work somewhat like an ISO 9000 standard. It represents an internally developed, self-guarantee which is not mandatory but which may well facilitate sales to discriminating users. 5. First Steps The first steps in this effort must be an effort to determine the feelings within the modeling community about these different issues. The small informal poll taken in May/June, 1994 made it clear that a majority felt validation to be an important issue, which so far has been neglected. In order to make a more detailed assessment of the community's feelings, we are proposing a 1 1/2 day open meeting at which the issues can be discussed and some plan of action developed. This meeting is to be held on Wednesday and Thursday, November 9 and 10, 1994, at the Holiday Inn at the Baltimore-Washington International (BWI) airport. There will be a registration fee of $100 per person, payable to Pool, Heller and Milne, Inc., 9520 Linden Avenue, Bethesda, MD, 20814 (Phone: 301-493-6595; FAX: 301-897-3487; Internet: Pool@phm.com). A corporate rate of $89 (plus tax) has been obtained at this hotel which will also provide meeting facilities and lunch for attendees. The BWI airport was selected as a site because various airlines, notably Southwest, offer very economical fares to BWI. Some support for this meeting has been provided by vendors and users of molecular modeling software . 6. Draft Agenda Workshop on CAMD Software Validation November 9-10, 1994 Agenda November 9 9:00 - 9:45 Introduction, Overview, Focus and Goals 1. Areas of validation 2. Models for validation 3. Validation support 4. Promulgation of validation data 9:45 - 10:30 Force Field Validation 10:30 - 10:45 Break 10:45 - 11:30 Validation of Small Molecule Modeling 11:30 - 12:15 Validation of Macromolecule Modeling 12:15 - 1:30 Lunch 1:30 - 2:15 Validation in Drug Design 2:15 - 3:00 Validation in Polymer and Materials Science 3:00 - 3:15 Break 3:15 - 5:15 Roundtable Discussion of Validation - Users' Perspective 1. One hour of short statements by Representatives from Industry, Government and Academia who are Users and not Developers. 2. One hour of Open Discussion Evening - Free for informal discussions November 10 9:00 - 10:30 Roundtable Discussion of Validation - Vendors' Perspective: 1. One hour of Short Statements by Representatives from Vendor Companies. 2. One hour of Open Discussion 11:30 - 12:30 Open Discussion. 1. Formulation of Conclusions and Goals and Preparation of a Final Statement which will be Appended to the Symposium Report for Subsequent Publication. Please address all technical questions and issues to A.J. Hopfinger, University of Illinois at Chicago, Department of Medicinal Chemistry and Pharmacognosy, (m/c 781), College of Pharmacy, 833 S. Wood Street, Chicago, IL 60612-7231, Phone: (312) 996 4816, Fax: (312) 413 3479, email: hopfinger@tony.pmmp.uic.edu Hitesh Patel MMaDD & QSAR lab Dept. of Med. Chem. & 'Cognosy UIC From gmeier@ncsa.uiuc.edu Tue Sep 20 14:59:05 1994 Received: from newton.ncsa.uiuc.edu for gmeier@ncsa.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id OAA07455; Tue, 20 Sep 1994 14:20:46 -0400 Received: from [128.254.136.231] by newton.ncsa.uiuc.edu with SMTP id AA13593 (5.65a/IDA-1.4.2 for chemistry@ccl.net); Tue, 20 Sep 94 13:20:22 -0500 Message-Id: <9409201820.AA13593@newton.ncsa.uiuc.edu> X-Sender: u34065@141.142.2.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Sep 1994 14:23:20 -0600 To: chemistry@ccl.net From: gmeier@ncsa.uiuc.edu (Gary Meier) Subject: Prediction of Protein Crystallinity Are there any algorithms, or rules of thumb, for estimating from a protein sequence the likelihood that the protein will crystallize? Can we study patterns of hydrophobic residues or some other feature(s) contained in the sequence and predict if the protein will crystallize? If so, can we suggest reasonable crystallization conditions to try? How might conditions differ if crystallization of a protein dimer is desired? Also, how might selection of a ligand for co-crystallization affect the odds of crystallization success? Is the highest affinity ligand necessarily the best choice, or are there good reasons for selecting a highly crystalline ligand, more hydrophobic ligand, etc.? I realize that there is a lot of art behind the science of protein crystallization, but if those of you with experience in this area can pass along any pearls of wisdom, I'll be happy to summarize them for the net. Gary Meier, Ph.D. (gmeier@ncsa.uiuc.edu) Senior Research Computational Scientist FMC Corporation, Agricultural Chemical Group Box 8 Princeton, NJ 08543 (609) 951-3448 From h.rzepa@ic.ac.uk Tue Sep 20 15:01:39 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id OAA08165; Tue, 20 Sep 1994 14:45:16 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <04132-0@punch.ic.ac.uk>; Tue, 20 Sep 1994 19:43:22 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA13851; Tue, 20 Sep 94 19:44:25 +0100 X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Sep 1994 19:44:34 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: http://www.nih.gov/molecular_modeling/mmhome.html During the summer, a number of chemical WWW sites have been actively preparing some fascinating materials for instructional and research use. These have been splendidly collected at the NIH, with pointers to some of the other sites. I highly recommend a browse through this material. Already, I believe it has enough "critical mass" to be useful in various chemistry courses. Image if the material increases ten fold or more, and most importantly has some form of quality assessment applied, how all of our teaching might change! I intend, if I have time, to incorporate some of this into the WWW94 presentation I will make at Chicago, to try to persuade the rest of the world, and any funding agencies listening, that the chemical Web is starting to mature, and to produce heavyweight material that no-one can afford to ignore. Again, anyone who knows of as yet unadvertised or unknown sources of good material, please send the URLs to me or the other coordinators of this stuff so that we can all share it. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.03, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804 World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From rickr@scripps.edu Tue Sep 20 15:59:04 1994 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.9/930601.1506) id PAA09594; Tue, 20 Sep 1994 15:18:34 -0400 Received: from ppg.scripps.edu by scripps.edu (5.61/1.34) id AA13871; Tue, 20 Sep 94 12:18:25 -0700 Received: by ppg.Scripps.EDU (4.1/SMI-4.1) id AA00728; Tue, 20 Sep 94 12:01:35 PDT Date: Tue, 20 Sep 94 12:01:35 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9409201901.AA00728@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: virus protection from Internet FTP Folks, Greetings. I know this is not a direct computational chemistry question but I think it is a concern to all. I was wondering if folks would be willing to share how they protect themselves from viruses that could be imported via anonomous FTP to their: UNIX workstations; Personal Computers; or Macintosh Computers. I would be very glad to summarize for the net if their is interest. To avoid swamping the net, perhaps folks could send answers to me directly first. Thanks a bunch. Rick Ross rickr@ppg.scripps.edu PPG Industries P.O. Box 9 Allison Park, PA 15101 From haney@netcom.com Tue Sep 20 16:00:25 1994 Received: from netcom16.netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id PAA10606; Tue, 20 Sep 1994 15:50:22 -0400 Received: by netcom16.netcom.com (8.6.9/Netcom) id LAA06128; Tue, 20 Sep 1994 11:53:22 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199409201853.LAA06128@netcom16.netcom.com> Subject: High School Chemistry To: CHEMISTRY@ccl.net Date: Tue, 20 Sep 1994 11:53:22 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1606 Chemistry Educators: How interesting that we see a post from Robert Gotwals on what methods we should provide to high school students and another post from a high school student, Daniel Mulcrone. It is my impression that while we have some very fancy simulation tools that we could provide these young students, there are details missing from some of these codes. I expect that many of the needs of high school students are more like the question of Daniel's dealing with what the elements are used for and how they fit into the periodic table. It seems to me that the items that one should focus on for high school chemistry should be simple building and display of molecules (including display of orbitals), and the periodic table. I have seen various periodic table programs, but none that could provide an encyclopedia of information about each element. It would be useful if one could combine the multimedia approach that was being demonstrated by IBM for several years along with the encyclopedia approach (ala ENCARTA) focusing on chemistry. While delivering the concept of molecular motion by introducing dynamics could be very powerful, one would have to be careful about theoretical discussions of such topics that contain so many approximations. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From evaldera@inti.ivic.ve Tue Sep 20 17:59:05 1994 Received: from inti.ivic.ve for evaldera@inti.ivic.ve by www.ccl.net (8.6.9/930601.1506) id RAA12016; Tue, 20 Sep 1994 17:11:24 -0400 Received: by inti.ivic.ve (AIX 3.2/UCB 5.64/4.03) id AA14565; Tue, 20 Sep 1994 17:01:38 +0100 Date: Tue, 20 Sep 1994 17:01:38 +0100 From: evaldera@inti.ivic.ve (Elmer Valderrama) Message-Id: <9409201601.AA14565@inti.ivic.ve> To: CHEMISTRY@ccl.net Subject: Chromium Cc: evaldera@inti.ivic.ve Hi dear netters, Does anyone know of a calcn for Cr at the CI.or.MBPT.or.CoupledCluster level? DFT.or.ThomasFermi for this atom may be also useful. Thanks in advance, Elmer Elmer Valderrama -Centro de Quimica- * IVIC * Caracas Venezuela* From szeinfel@snfma2.if.usp.br Tue Sep 20 18:06:40 1994 Received: from snfma2.if.usp.br for szeinfel@snfma2.if.usp.br by www.ccl.net (8.6.9/930601.1506) id RAA12384; Tue, 20 Sep 1994 17:45:53 -0400 Received: (szeinfel@localhost) by snfma2.if.usp.br (8.6.8/8.6.4) id SAA19035; Tue, 20 Sep 1994 18:39:17 -0300 Date: Tue, 20 Sep 1994 18:39:16 -0300 (EST) From: Rafael Iosef Najmanovich Szeinfeld {S To: computational chemistry Subject: Q.M & protein folding Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Could someone recomend fundamental papers appling Quantum Mechanics to protein folding. Thanks in advance, Rafael. *----------------------------------------------------- * Rafael Iosef Najmanovich Szeinfeld * Dept. Biochemistry -Chemistry Institute * Dept. Mathematical Physics -Physics Institute * University of Sao Paulo * E-MAIL : szeinfel@snfma1.if.usp.br * * MAIL: Depatartamento de Bioquimica - BLOCO 10 INF. * Universidade de Sao Paulo * Av. Prof. Lineu Prestes 748 * CEP 05508-900 Sao Paulo - SP - Brazil *------------------------------------------------------ From szeinfel@snfma2.if.usp.br Tue Sep 20 18:07:19 1994 Received: from snfma2.if.usp.br for szeinfel@snfma2.if.usp.br by www.ccl.net (8.6.9/930601.1506) id RAA12337; Tue, 20 Sep 1994 17:40:58 -0400 Received: (szeinfel@localhost) by snfma2.if.usp.br (8.6.8/8.6.4) id SAA18938; Tue, 20 Sep 1994 18:34:12 -0300 Date: Tue, 20 Sep 1994 18:34:12 -0300 (EST) From: Rafael Iosef Najmanovich Szeinfeld {S To: Hopfinger at UICVM cc: chemistry@ccl.net Subject: Re: CCL:Validation of Modeling Software In-Reply-To: <199409201745.NAA06659@www.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I think that a fundamental step in validating modeling softwares (MSoft's) is to compare the output from different softwares any attempt to compare with the reality. Sincerly yours, Rafael. *----------------------------------------------------- * Rafael Iosef Najmanovich Szeinfeld * Dept. Biochemistry -Chemistry Institute * Dept. Mathematical Physics -Physics Institute * University of Sao Paulo * E-MAIL : szeinfel@snfma1.if.usp.br * * MAIL: Depatartamento de Bioquimica - BLOCO 10 INF. * Universidade de Sao Paulo * Av. Prof. Lineu Prestes 748 * CEP 05508-900 Sao Paulo - SP - Brazil *------------------------------------------------------ From chen@agouron.com Tue Sep 20 19:59:01 1994 Received: from agouron.com for chen@agouron.com by www.ccl.net (8.6.9/930601.1506) id TAA13735; Tue, 20 Sep 1994 19:03:36 -0400 Received: from agouron.agouron.com by agouron.com via SMTP (940715.SGI.52/930901.SGI) for chemistry@ccl.net id AA18806; Tue, 20 Sep 94 16:04:23 -0700 Received: from localhost by agouron (8.6.4.2/10.3) id QAA11726; Tue, 20 Sep 1994 16:04:21 -0700 Date: Tue, 20 Sep 1994 16:04:21 -0700 From: chen@agouron (Chris Chen) Message-Id: <199409202304.QAA11726@agouron> To: chemistry@ccl.net Subject: SEAL Dear netters: Do anyone know any recent papers about SEAL calculation? Appreciate. Chris Chen chen@agouron.com -- San Diego, California the finest city in the States