From p.mencarelli@caspur.it Thu Dec 14 06:28:47 1995 Received: from axcasp.caspur.it for p.mencarelli@caspur.it by www.ccl.net (8.6.10/950822.1) id GAA13863; Thu, 14 Dec 1995 06:20:11 -0500 Date: Thu, 14 Dec 1995 06:20:11 -0500 Message-Id: <199512141120.GAA13863@www.ccl.net> Received: from aldebaran.sci.uniroma1.it by axcasp.caspur.it with SMTP; Thu, 14 Dec 1995 12:03:05 GMT X-Sender: mencarel@axcasp.caspur.it X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "Dr. Paolo Mencarelli" Subject: rotational entropy in solution Hi all, I am an organic chemist interested in host-guest chemistry, and I have the problem of evaluate the rotational entropy of a molecule in solution. I am able to evaluate the rotational entropy in the gas phase by using statistical thermodynamics, i.e. by the rotational partition function, but I am not aware of extension of such theory to the liquid state. Does anyone know how to evaluate, even in approximate way, the rotational entropy of a molecule in solution? Thanks. Paolo Mencarelli ===================================== Dr. Paolo Mencarelli Dipartimento di Chimica Universita' La Sapienza P.le Aldo Moro, 2 00185 Roma - ITALY tel 06-49913697 fax 06-490631 E-Mail p.mencarelli@caspur.it E-Mail mencarel@xantia.caspur.it ===================================== From owner-chemistry@ccl.net Thu Dec 14 07:13:48 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA14296; Thu, 14 Dec 1995 07:03:42 -0500 Received: from WAPinorg.chemie.uni-halle.de for ariane@WAPinorg.chemie.uni-halle.de by bedrock.ccl.net (8.7.1/950822.1) id HAA24137; Thu, 14 Dec 1995 07:03:38 -0500 (EST) Received: by WAPinorg.chemie.uni-halle.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id MAA16187; Thu, 14 Dec 1995 12:35:18 +0100 Date: Thu, 14 Dec 1995 12:35:18 +0100 From: ariane@WAPinorg.chemie.uni-halle.de (Ariane) Message-Id: <199512141135.MAA16187@WAPinorg.chemie.uni-halle.de> To: chemistry@ccl.net Subject: CCL:how construct aux. dft bases Dear colleagues, since I'm a rather new user of density functional methods I've problems in generating proper auxiliary bases for the fitting of the charge density and/or xc-part in native dft-codes (deMon, DeFT, DGauss, ...) for traditional HF basis sets not introduced into the corresponding basis libraries of these programs. Are there any common rules for preparing such bases sets, likely as an exponential bases expansion ? Anyone who share her/his knowledge with me/us are welcome. Regards Ariane From owner-chemistry@ccl.net Thu Dec 14 08:58:49 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA14842; Thu, 14 Dec 1995 08:53:33 -0500 Received: from harfang.CC.UMontreal.CA for wangyo@CHIMCN.UMontreal.CA by bedrock.ccl.net (8.7.1/950822.1) id IAA24824; Thu, 14 Dec 1995 08:53:27 -0500 (EST) Received: from chims1.CHIMCN.UMontreal.CA (chims1.CHIMCN.UMontreal.CA [132.204.11.106]) by harfang.CC.UMontreal.CA with ESMTP id IAA20764 (8.6.11/IDA-1.6); Thu, 14 Dec 1995 08:52:52 -0500 Received: by chims1.CHIMCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id NAA21953; Thu, 14 Dec 1995 13:53:31 GMT Date: Thu, 14 Dec 1995 08:53:31 -0500 (EST) From: Wang Youliang Subject: Re: CCL:G:UHF v.s. ROHF To: "JDA03546@niftyse" cc: chemistry@ccl.net In-Reply-To: <199512140333.MAA17221@inetnif.niftyserve.or.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 14 Dec 1995, JDA03546@niftyse wrote: > (Large output part was snipped.) > I posted this yesterday and have already received some replies. > I really appreciate those who responded! > I'm sorry that I forgot to say an important thing. Since my purpose > is to compare UHF and ROHF, the system has to be open shell. So the > calculation was done in triplet state and both UHF and ROHF gave the > S**2 value exactly 2. I'll summarize the answers. > Thank you. > ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <12/14 09:38> ** > Your problem is due to single-determinant wavefunction. You can simply test the stability of wavefunction for UHF calculations by using STABLE=OPT (or other options, see Gaussian Manual for details). Good lucky Y. Wang wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww w email: wangyo@chimcn.umontreal.ca w w Web: http://www.centrcn.umontreal.ca/~wangyo w wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww From owner-chemistry@ccl.net Thu Dec 14 09:07:59 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA14830; Thu, 14 Dec 1995 08:52:49 -0500 Received: from newton.ncsa.uiuc.edu for balajiv@ncsa.uiuc.edu by bedrock.ccl.net (8.7.1/950822.1) id IAA24821; Thu, 14 Dec 1995 08:52:46 -0500 (EST) Received: from actually.ncsa.uiuc.edu (actually.ncsa.uiuc.edu [141.142.221.71]) by newton.ncsa.uiuc.edu (8.6.11/8.6.12) with ESMTP id HAA09734; Thu, 14 Dec 1995 07:52:33 -0600 Received: by actually.ncsa.uiuc.edu (8.6.9/NCSA-4.1) id HAA01254; Thu, 14 Dec 1995 07:52:30 -0600 Date: Thu, 14 Dec 1995 07:52:30 -0600 From: balajiv@ncsa.uiuc.edu (Balaji Veeraraghavan) Message-Id: <199512141352.HAA01254@actually.ncsa.uiuc.edu> To: chemistry@ccl.net Subject: GAUSSIAN 94 WORKSHOP Forwarding: Mail from 'gaussian.com!fox@lorentzian.com (Doug Fox)' dated: Thu, 14 Dec 1995 01:18:32 -0500 (EST) ************************************************************************* The National Center for Supercomputing Applications and Silicon Graphics Computer Systems, Inc. are pleased to announce: INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE Date: February 27 - March 1, 1996 Location: Silicon Graphics, Inc. Mountain View, Ca. The National Center for Supercomputing Applications (NCSA) in conjunction with Silicon Graphics, Inc. (SGI) are pleased to sponsor "Introduction to Gaussian: Theory and Practice." This workshop will be presented in conjunction with Gaussian, Inc. and Semichem, Inc., from February 27 to March 1, 1996 in the SGI facilities in Mountain View, California. The workshop will cover the full range of methods available in the Gaussian package with emphasis on new methods and features which make Gaussian applicable to an ever widening spectrum of research applications. The workshop is structured to provide an introduction to electronic structure theory as well as a hands-on review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. Instructors: Prof. Gustavo Scuseria Rice University Prof. George A. Petersson Wesleyan University Dr. Douglas J. Fox Gaussian, Inc. Dr. Roberto Gomperts Silicon Graphics, Inc. Dr. Balaji Veeraraghavan NCSA Tentative Agenda Topics: Introduction to Electronic Structure Theory Model Chemistries: A Framework for Understanding Electronic Structure Theory Results MCSCF Methods and Applications Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Excited States via CI Singles Thermochemistry via Model Chemistries Interpretation of Gaussian 94 Results Predicting Molecular Properties Solvent Effects on Molecular Electronic Structure Gaussian Utilities Estimating Resource Requirements There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of an SGI workstation to complete exercises, experiment and/or conduct short research topics. Each workshop participant will also be provided a copy of the lecture notes and a copy of the Gaussian 94 User's Reference. ---------------------------------------------------------------------------- APPLICATION PROCEDURE All applicants must submit the attached application form and a cover letter which briefly (one or two paragraphs) describes your current research and how participating in this workshop will enhance your research. The cover letter should also include one or two sentences indicating your level of experience with computers. Seats are limited and the potential applicants are encouraged to send the application material ASAP. Costs: Workshop registration: $250.00 Hotel accomodations: A list of hotel accomodations in the vicinity of the SGI facility will be made available to all registrants. Hotel accomodations will be the responsibility of each participant. A list of nearby hotels will be provided upon registration, local transportation will also be arranged. Meals: Meals will be the responsibility of each participant. PLEASE RETURN YOUR APPLICATION MATERIALS TO: Workshop coordinator Gaussian, Inc. Carnegie Office Park Bldg. 6, Suite 230 Pittsburgh, PA 15106 USA Additional information can be obtained from Telephone: (412) 279-6700 Fax: (412) 279-2118 Email: info@gaussian.com DEADLINES: Receipt of Registration Materials: February 9, 1996 APPLICATION FORM: Name: Affiliation: Address: Telephone: Facsimile: E-Mail Address: Nationality: Passport Number (for noncitizens): Machine and User Account Name: Please indicate your Research Standing (check one): Faculty _______ Postdoctorate _______ Graduate Student ______ Undergraduate Student _______ University Research Staff _______ University Non-Research Staff ______ Government _______ Industrial ______ Other ______ Remember to include the cover letter with the additional information. -------------------------------------------------------------------------- This notice is sent without warranty of any kind, expressed or implied by Gaussian, Inc. or SGI. Gaussian is a trademark of Gaussian, Inc. **************************************************************************** ----------------------------------------------------------------------- Balaji Veeraraghavan, Ph. D. Phone : 217-333-2754 Research Programmer, Chemistry Fax : 217-244-2909 NCSA email : balajiv@ncsa.uiuc.edu 4151 Beckman Institute 405 N. Mathews Avenue Urbana, IL 61801 ----------------------------------------------------------------------- From moshe_o@VNET.IBM.COM Thu Dec 14 09:58:55 1995 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.10/950822.1) id JAA15545; Thu, 14 Dec 1995 09:46:09 -0500 Message-Id: <199512141446.JAA15545@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R3) with BSMTP id 9861; Thu, 14 Dec 95 09:45:47 EST Date: Thu, 14 Dec 95 16:44:01 IST From: "Moshe Olshansky" To: chemistry@www.ccl.net Subject: Improving performance of the HARTREE-FOCK SCF ROOTHAAN Computations. Dear netters, We are offering a technique/code which accelerates the solution of the above equations considerably (factors of about x2-x5 have been obtained, depending on specific example). The technique is offered to organizations owning a source-code of a Hartree Fock package (whether a user in the chemical industry or a company which develops/sells such packages/codes). We shall install our technique/ code on top of that code, provided a mutual commercial agreement with IBM has been reached. CONTACT: Dr. Moshe Olshansky (moshe_o@vnet.ibm.com) IBM Israel Science & Technology LTD. MATAM- Advanced Technology Center Haifa 31905, Israel Fax: (972)-4-8550070 From acp37@rs1.rrz.Uni-Koeln.DE Thu Dec 14 11:28:51 1995 Received: from rs1.rrz.Uni-Koeln.DE for acp37@rs1.rrz.Uni-Koeln.DE by www.ccl.net (8.6.10/950822.1) id LAA17949; Thu, 14 Dec 1995 11:26:07 -0500 Received: by rs1.rrz.Uni-Koeln.DE id AA47130 (5.67b/IDA-1.5 for CCL ); Thu, 14 Dec 1995 17:25:36 +0100 Date: Thu, 14 Dec 1995 17:25:36 +0100 (MET) From: "T. Koch" To: CCL Subject: SUMMARY: How to measure stability? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Dear netters, some times ago I posted a question concerning the stabilty of computed=20 molecules. I received some answers and would like to thank all who responded. Now I=20 post the answers I got. If there are any additional opinions on this=20 topic I would appreciate to receive your mail. The original posting was: I have a question which should be of considerable interest for=20 computational chemists. The question is: How do I measure computationally= =20 the stability of organic molecules? I study some molecules which presumably have not yet been prepared. And I= =20 would like to know if these molecules have a chance to exist. What I did=20 so far is the most simple and obvios method: I compared the absolute=20 electronic energy with the same quantity on a known and more or less=20 stable isomer. But from the results I got I think that this is only a=20 crude approximation on a "measure" of stability and reactivity. What I didn't examine yet but could be quite sensible (I think) is doing= =20 a CI or MCSCF calculation and looking at the energy gap between the=20 frontier orbitals and comparing it to known isomers. Another way could be an examination of the computed IR-spectrum. Are=20 there very low frequencies (shallow dips in the potential engergy=20 surface) which could lead to "new" molecules? Is there a way to determine "centers of reactivity" ? =20 The answers are: From: Ernest Chamot >I have a question which should be of considerable interest for=20 >computational chemists. The question is: How do I measure computationally= =20 >the stability of organic molecules? Actually, your initial approach should give you a decent estimate of the thermodynamic stability (especially the RELATIVE thermodynamic stability), but as you point out it is a poor measure of the KINETIC stability/reactivi= ty: >so far is the most simple and obvios method: I compared the absolute=20 >electronic energy with the same quantity on a known and more or less=20 >stable isomer. But from the results I got I think that this is only a=20 >crude approximation on a "measure" of stability and reactivity. This thermodynamic stability would give you a good idea of whether the reactions you are proposing to synthesize the new compound will work, but not whether the new compound will be isolable before conversion into something else. In the past I've considered each bond individually and calculated the energ= y barrier for each bond homolysis in systems where bond homolysis was the onl= y reasonable mode of decomposition. You could similarly consider all reasonable reactions (homolysis, heterolysis, cyclic ring reversions, dimerizations, etc.) one by one, but if you have a very complicated system this could be daunting. (Using CI or MCSCF may get you a more accurate answer, but if it reduces the number of possibilities you can test, I think it would reduce rather than increase your confidence that you understand th= e stability of your system.) What one needs, of course, is a good enough ide= a of the entire potential energy surface, to be able to identify the lower(est) saddle points serving as barriers between your molecule and conversion into some other isomer/products. This is sort of what you would be doing with: > Another way could be an examination of the computed IR-spectrum. Are=20 >there very low frequencies (shallow dips in the potential engergy=20 >surface) which could lead to "new" molecules? > Is there a way to determine "centers of reactivity" ? I think it would be a good idea to pursue, but not just looking at the lowest energy frequencies: one vibrational mode may start out steeper than the others, but crossover a transition state to some other products before going through as high a maximum. The low frequencies would be good startin= g points though. I haven't tried following a specific eigenvector from a ground state as such (I'm usually either starting from a transition state o= r near to a stationary geometry), but I would think Intrinsic Reaction Coordinate (or DRC) searches following each of the lower frequencies from the computed IR-spectrum would be a good way to probe for the preferred "centers of reactivity" without having to explicitly define the center of reactivity a priori. From: Pascal HEBANT > Is there a way to determine "centers of reactivity" ? You can use Fukui functions that are easy to compute from HF or DFT calculations. see among other references : J. L. G=E1zquez, Hardness and softness in Density Functional Theory in Chemical Hardness , Coll. Structure and Bonding (Springer-Verlag, Berlin, 1993) R. G. Parr et W. Yang, Density Functional Theory of atoms and molecules , (Oxford University Press, New York, 1989) P. K. Chatteraj et R. G. Parr, Density Functional Theory of chemical hardness in Chemical Hardness , Coll. Structure and Bonding (Springer-Verlag, Berlin, 1993) From: Jason Lye Our group has recently begun to look at predicting the regioselectivity of= =20 certain nucleophilic and electrophilic reactions. Most techniques use a=20 weighted frontier orbital approach. Some references that you might want to read are: K. Fukui, T. Yonezawa, C. Nataga, Journal of Chemical Physics, Vol 26, No.4 Pages 831-841, (1957) K. Fukui, T. Yonezawa, C. Nataga, H. Shingu,=20 Journal of Chemical Physics, Vol 22, No.8, Pages 1433-1442, (1954) K. Fukui, T. Yonezawa, C. Nataga, Bulletin of the Chemical Society of Japan= , Vol. 27, Pages 423-427, (1954) Also, we have learned that other factors besides frontier orbital density a= re often involved. These may include steric effects and also electrostatic=20 repulsion/attractions between the two reagents. From: "E. Lewars" With regard to the recent question by Thorsten Koch "How do I measure the stability of organic molecules? ...I compare absolute electronic energy wit= h... a known and more or less stable isomer." There were also queries about the relevance of frontier orbitals and calculated IR frequencies. *Stability* can refer to (1) the tendency of an isolated molecule to reac= t, perforce by isomerizing or by dissociating, or it can refer to (2) the tend= ency of a molecule to react with another (possibly identical) molecule. Considering (1): The calculated freqs (i.e. the calc IR spectrum) provide information abou= t the reactivity of the isolated molecule. If there are no imaginary ("negat= ive") freqs, the molecule can exists *as far as that particular level of calc is concerned*, that is, it is a relative minimum on the potential energy surfa= ce; it sits in a well and jiggles its all-real vibrational modes, escaping from the well at a rate that, ignoring wierd things like tunneling, depends (at least approximately) on the height of the barrier separating it from the nearest other well (or nearest plateau, for dissociation). A low-freq vibration corresponding to bond cleavage should make one suspe= ct that at some higher computational level this freq will become imaginary, an= d the bond will actually break. A low-freq "vibration" that coresponds to a torsional mode would, if it were coaxed into being imaginary at a higher le= vel, correspond to a conformational change: the molecule might still exist, but = might not, say, be flat as in the input geom, but rather puckered (e.g. flat D4h cyclobutane may prefer to be D2d). The stability of a real molecule (a relative minimum) can be quantified b= y calculating the rate at which it goes over the lowest barrier separating it >from its isomerization or dissoaciation product(s). Of course, if it's substantially the lowest-energy species on the PES then you don't have to w= orry about this. Stability is most intelligible if expressed as half-life at so= me temperature (like room temp, where most of us live). Considering (2): Comparison of the frontier orbitals (HOMO and LUMO) with those of known, similar molecules is probably wothwhile, since reaction with electrophiles and nucleophiles will be governed (to the ubiquitious first approximation) by the energies of these orbitals. Some references to calulations on the stabilities/existence of exotic organ= ic molecules are: Oxirene and substituted oxirenes-- Vacek,..., Schaefer,..., J Phys Chem 98 (1994) 8660. Fowler, Galbraith, Vacek and Schaefer, J Am Chem Soc 116 (1994) 9311. Scott, Nobes, Schaefer and Radom, J Am Chem Soc 116 (1994) 10159 N6 (e.g. hexaazabenzene), N8, etc-- Engelke, J Am Chem Soc 115 (1993) 2961 Engelke, J Org Chem 57 (1992) 4841 Engelke and Stine, J Phys Chem 94 (1990) 5689 ["Is N8 Cubane Stable?] Engelke, J Phys Chem 94 (1990) 6924 /|\ Engelke, J Phys Chem 96 (1992) 10789 | Engelke, J Phys Chem 93 (1989) 5722 | STABLE Benzooxirene-- Lewars, THEOCHEM 1996 CO2 polymers-- Lewars, THEOCHEM 1996 /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer Physikalische Chemie II der Universitaet zu Koeln | | Luxemburger Str. 116, 50939 Koeln, Germany | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ From owner-chemistry@ccl.net Thu Dec 14 13:58:53 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA19840; Thu, 14 Dec 1995 13:49:21 -0500 Received: from relay-4.mail.demon.net for davel@chmqst.demon.co.uk by bedrock.ccl.net (8.7.1/950822.1) id NAA27641; Thu, 14 Dec 1995 13:49:00 -0500 (EST) Received: from post.demon.co.uk by relay-4.mail.demon.net id sg.ab09665; 14 Dec 95 18:32 GMT Received: from chmqst.demon.co.uk by relay-3.mail.demon.net id sg.aa29141; 14 Dec 95 18:31 GMT From: David Livingstone Organization: ChemQuest To: chemistry@ccl.net Date: Thu, 14 Dec 1995 08:57:31 +0100 Subject: (Fwd) Re: CCL:Octanol/Water Partitioning Reply-to: davel@chmqst.demon.co.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) X-SMTP-Posting-Host: chmqst.demon.co.uk [Thu, 14 Dec 95 18:31:21 GMT] Message-ID: <9512141831.sg.aa29141@relay-3.mail.demon.net> X-SMTP-Posting-Host: post.demon.co.uk [Thu, 14 Dec 95 18:32:18 GMT] I sent this answer back to Thomas directly but thought it was worth posting to the list as others might find this information useful. Dave. Date: Fri, 17 Nov 1995 10:43:20 Thomas R. Cundari writes: > Are there any basic introductory articles which describe water/octanol > partition coefficients? > > >From what little I have read, it seems they are a popular measure of > hydrophilicity of a compound and > are also popular in structure-activity studies since a large number of them > databased by the folks > at Pomona. It's nice to see someone "discovering" log P. Yes, partition coefficients are a pretty popular parameter for QSAR - I reported that in 1988 over 40% of the 337 studies listed in the QSAR journal and its abstract service involved a hydrophobicity descriptor (D.J. Livingstone, "Quantitative Structure-Activity Relationships" in: Similarity Models in Organic Chemistry, Biochemistry and Related Fields (Eds, R.I. Zalewski, T.M. Krygowski & J. Shorter), Elsevier, 1991, pp 557-627). There is a bit of discussion of log P measurement and calculation in this chapter, along with a few references. > > Mainly I'm interested in knowing how to do the experiments to measurw logP. > Are the experiments involved? Any applications/examples for metal > complexes would be most interesting. > There are numerous reviews and introductory articles that deal with the experimental determination of log P, far too many to list here, but some good places to look are: Chapter 4 (The hydrophobic parameter: measurement and calculation) of the new book by Hansch & Leo (Exploring QSAR Fundamentals and Applications in Chemistry and Biology, ACS, 1995, ISBN 0-8412-2987-2) "Partition Coefficient Determination and Estimation", (Eds W. Dunn, J. Block & R. Pearlman), Pergamon, 1986, ISBN ???? The chapter by Peter Taylor in that mammoth multi-volume set "Comprehensive Medicinal Chemistry.......". It is actually in Vol. 4 (Quantitative Drug design (ed. C.A. Ramsden) Pergamon, Oxford, 1990, pp 241-294) Chapter 3 (Parameters) of Hugo Kubinyi's book (QSAR: Hansch Analysis and related Approaches, VCH, Weinheim, 1993, ISBN 3-527-30035-X). Partition coefficients are actually very easy and very difficult to measure ! I hope this helps. Cheers, Dave. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Cheyney House, 19-21 Cheyney St., Steeple Morden. Herts UK SG8 0LP Phone & Fax: +44 (0)1763 852569 e-mail davel@chmqst.demon.co.uk ------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Dec 14 15:45:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA22424; Thu, 14 Dec 1995 15:32:17 -0500 Received: from uscmail.usc.es for qfsaulo@usc.es by bedrock.ccl.net (8.7.1/950822.1) id PAA28841; Thu, 14 Dec 1995 15:32:08 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA06161; Thu, 14 Dec 1995 21:32:48 +0100 Date: Thu, 14 Dec 1995 21:32:48 +0100 From: qfsaulo@usc.es (Saulo Vazquez Rodriguez) Message-Id: <199512142032.AA06161@uscmail.usc.es> To: chemistry@ccl.net Subject: SUMMARY:RRKM Last week I had asked for the UNIMOL suite of programs or any program to calculate unimolecular rate constants. I am very grateful to all the people who replied to my original request, especially to Professor Gilbert whose response is shown below. Saulo Vazquez (qfsaulo@usc.es) Thank you for your enquiry about obtaining our UNIMOL suite by email. That can be done using FTP. To run the program suite, you will also need the manual, which is some 30 pages in length. This manual can also be sent to you electronically, most easily as a Macintosh binhex file which can then be printed out. Note also that the program and manual make frequent reference to our text, "Theory of unimolecular and recombination reactions". R.G. Gilbert and S.C. Smith. Blackwell Scientific Publications, Oxford and Cambridge Mass., 1990. Users have found having access to this text makes the program much easier to understand. To access UNIMOL programs and sample data files: ftp to ftp.chem.usyd.edu.au as ftp or anonymous Change Directory to /pub/unimol copy all of the files in this directory. This contains the program file. The subdirectory doc contains the documentation, both as a Macintosh BinHex file or as an RTF ("rich-text format") file which can be read into any word processor. These are available as manual.hqx and manual.rtf For further details, email gilbert@chem.usyd.edu.au Robert G Gilbert Professor Robert G Gilbert Sydney University Polymer centre Chemistry School, Sydney University. NSW 2006 Australia phone: 61-2-351 3366. fax: 61-2-351 3329 From owner-chemistry@ccl.net Thu Dec 14 17:00:15 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id QAA23346; Thu, 14 Dec 1995 16:49:03 -0500 Received: from laura.harvard.edu for stahl@laura.harvard.edu by bedrock.ccl.net (8.7.1/950822.1) id QAA29581; Thu, 14 Dec 1995 16:48:56 -0500 (EST) Received: by laura.harvard.edu; (5.65/1.1.8.2/16Mar95-8.2MPM) id AA20556; Thu, 14 Dec 1995 16:48:55 -0500 Date: Thu, 14 Dec 1995 16:48:54 -0500 (EST) From: Matt Stahl X-Sender: stahl@laura.harvard.edu To: chemistry@ccl.net Subject: new software release - PADRE Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Netters, Pat Walters and I are releasing the latest program from BABEL, Inc. Here's the README file: PADRE - Copyright (C) 1994-1995 Matthew T. Stahl and W. Patrick Walters. All Rights Reserved. PADRE - Population Analysis and Duplicate Removal PADRE is a general purpose utility that can be used to analyse the results of conformational searches, and to measure similarity and differences between molecules. The program will be made available for a number of Unix platforms (Irix, Ultrix, Linux, more to come...). Some of the highlighted capabilities include: - molecular overlap based on sterics and electronics - cluster analysis - Tcl/Tk based dendogram viewer interface to RASMOL and other programs - automatic removal of duplicates from a multi-conformer file - RMS distance / torsional difference measurement - automatic detection of topologically equivalent atoms (automorphisms) - support for numerous input and output file types - simple command line interface Availability PADRE is freeware and can be retreived from the Ohio Supercomputer Center computational chemistry archive (www.ccl.net). Installation Retrieve the file padre_beta_(platform).tar.Z from www.ccl.net using either ftp or a web browser. ftp www.ccl.net login: anonymous password: your-e-mail-address cd /pub/chemistry/software/UNIX/PADRE binary get padre_beta_(platform).tar.Z quit 1. uncompress padre_beta_(platform).tar.Z 2. tar -xvf padre_beta_(platform).tar 3. follow the instructions in the PADRE.DOC ----------------------------------------------------------------------- Matthew Stahl, Ph.D., Harvard University, stahl@lhasa.harvard.edu Voice (617) 495-2654, Fax (617) 495-1823 "Illegitimi Non Carborundum" ----------------------------------------------------------------------- "Reintegration complete," ZORAC advised. "We're back in the universe again ..." An unusually long pause followed, "... but I don't know which part. We seem to have changed our position in space." A spherical display in the middle of the floor illuminated to show the starfield surrounding the ship. "Several large, artificial constructions are approaching us," ZORAC announced after a short pause. "The designs are not familiar, but they are obviously the products of intelligence. Implications: we have been intercepted deliberately by a means unknown, for a purpose unknown, and transferred to a place unknown by a form of intelligence unknown. Apart from the unknowns, everything is obvious." -- James P. Hogan, "Giants Star"