From CHAMANKHAH@sask.usask.ca Wed Sep 15 17:16:54 1993 Date: Wed, 15 Sep 1993 23:16:54 -0600 (CST) From: CHAMANKHAH@sask.usask.ca Subject: Again about Training and Pattern recognition Program To: chemistry@ccl.net Message-Id: <01H2ZTCV5AZS9N3YMW@SKYCAT.USask.CA> Dear netters; Could I ask those kind people who sent me very valuable information regarding: 1) Training programs available for popular molecular modeling softwares 2) A simple Pattern recognition software used for QSAR analysis to again send me their messages. I would really appreciate if this could be possible since at the time of summarizing and having it sent to the chemistry list, by mistake I lost some of them. I tried different ways to retrieve them but unfortunately not successful. I am looking forward to your responses, specially from Professor Martin, Abbott Lab, IL and the person who referred me to Professor Dunn III for the pattern recognition program. Again thank you very much and sorry for inconveniences this may cause for you. M.Chamankhah From VERDONK%HUTRUU54.BITNET@phem3.acs.ohio-state.edu Thu Sep 16 11:36:00 1993 Date: Thu, 16 Sep 1993 10:36 +0100 (MET) From: Marcel Verdonk Subject: Gibbs free energy of solvation To: chemistry@ccl.net Message-Id: <01H304TM89YQ8WZ9ZN@phem3.acs.ohio-state.edu> Dear mailers, I am interested in the Gibbs free (or Helmholtz) energy of the following process: MCl (vac) ----> MCl (aq) DG M represents a charged molecule (say serotoninH+). Cl is an arbitrary couter ion. DG must contain the change in Gibbs free energy of the complex as well as that of the water. Does anybody know of a simple and quick way to estimate DG (and references in literature)? I am specially interested in methods using (functional) group contributions, but other methods may be interesting as well. Best regards, Marcel Verdonk, Dept. of Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH UTRECHT, THE NETHERLANDS. From rossi@watson.ibm.com Thu Sep 16 00:57:15 1993 Message-Id: <9309160957.AA17683@nic-support.watson.ibm.com> To: chemistry@ccl.net Subject: ACS Computers in Chemistry Division -- Call for Posters Date: Thu, 16 Sep 93 05:57:15 -0500 From: "Angelo R. Rossi" ********************************************************* * * * AMERICAN CHEMICAL SOCIETY * * * * COMPUTERS IN CHEMISTRY DIVISION * * * * CALL FOR POSTERS * * * * Spring National ACS Meeting, San Diego, California * * * * March 13-18, 1994 * * * ********************************************************* This is a notice for people to submit abstracts for the ACS Computers in Chemistry Division (COMP) General Computational Chemistry Poster Session to be held at the Spring National ACS Meeting, March 13-18, 1994 in San Diego, California. Abstracts are due on the standard printed ACS Abstract Form by October 29, 1993 Because of programming limitations only abstracts for POSTERS in the General Computational Chemistry Session can be accepted. There will be no ORAL presentations. General Computational Chemistry; Poster Sessions - Dr. Angelo R. Rossi, IBM Research Division, T. J. Watson Research Center, Yorktown Heights, NY 10598; Tel: 914-945-3834; Fax: 914-945-2141; e-mail: rossi@watson.ibm.com From jaeric@mtcamm.monsanto.com Thu Sep 16 03:20:01 1993 From: Jon A. Erickson Message-Id: <9309161320.AA03564@mtcamm.monsanto.com> Subject: Charge-Transfer Complexes... To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Thu, 16 Sep 93 8:20:01 CDT Does anyone know of any references, programs, or other info on how to deal with geometries and energies of charge-transfer complexes? Currently, the approach I'm taking is semi-empirical- CI methods. Thanx in advance for any suggestions. -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. FAX: (314) 694-1080 # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From WMELCHIOR@fdant.nctr.fda.gov Thu Sep 16 03:24:37 1993 Date: Thu, 16 Sep 1993 8:24:37 -0500 (CDT) From: "Bill Melchior, NCTR/FDA" To: chemistry@ccl.net Message-Id: <930916082437.20200261@fdant.nctr.fda.gov> Subject: crystallographers' email addresses msjones@whale.st.usm.edu (Michael Sean Jones) asks: > I am searching for information on how to contact any of the authors >of a journal article with the following bibliographic information >published in The EMBO Journal in 1988. > > The 2.0A X-ray crystal structure of chicken egg white cystatin >and its possible mode of interaction with cysteine proteinases. The idea of using gopher was good, but not executed quite right. What you need to do is gopher to merlot.welch.jhu.edu, and go to item 14, searching for researchers. In that menu is a search for crystallographers, where you will find that Robert Huber is at G_HUBER@MPIB-MARTINSREID.MPG.DBP.DE (I don't know why it's "G_" instead of "R_", but that's what it says.) and that Bode, Engh, and Musil can all be reached at the same address by substituting the appropriate last name for G_HUBER. Cheers, Bill ________________________________________________________________________________ Views expressed are not necessarily those of NCTR, its sponsoring agencies, or the United States government. Bill Melchior || National Center for Toxicological Research || ALL statements Jefferson, AR 72079 || in this (501) 543-7206 || signature box || are false. WMELCHIOR@NTET.NCTR.FDA.GOV || From raman@bioc01.uthscsa.edu Thu Sep 16 03:41:09 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9309161341.AA22270@bioc01.uthscsa.edu> Subject: Re: Address Request To: msjones@whale.st.usm.edu (Michael Sean Jones) Date: Thu, 16 Sep 1993 08:41:09 -0500 (CDT) Mike: > I am searching for information on how to contact any of the authors > published in The EMBO Journal in 1988. > The 2.0A X-ray crystal structure of chicken egg white cystatin > and its possible mode of interaction with cysteine proteinases. > > Wolfram Bode, Richard Engh, Djordje Musil, Ulrich Thiele, Robert > Huber, Andrej Karshikov(1), Joze Brzin(2), Janko Kos(2) and > Vito Turk(2) Richard Engh can be reached at "engh@nmrvex.biochem.mpg.de" . He does work with Robert Huber and should be able to help you. Let me know if you have difficulties reaching him. I think Bode is still there, but could be mistaken. What you might want to try is finger nmrvex to find out if the parties you are interested in have an account there. Hope this helps. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From far@medinah.atc.ucarb.com Thu Sep 16 05:55:15 1993 Date: Thu, 16 Sep 1993 09:55:15 -0400 Message-Id: <9309161355.AA22599@medinah.atc.ucarb.com> To: CHEMISTRY@ccl.net From: far@medinah.atc.ucarb.com (Forrest Richey) Subject: NH3/Dichloroethane > Ethyleneamines Model I'm looking for a computational model of the reaction of ammonia with 1,2-dichloroethane. That is C-N bond formation between ammonia (and resulting intermediate amines) and 1,2-dichloroethane (EDC). The products, commonly known as ethyleneamines, contain a great number of homologs and isomers. What I want from the model is a product distribution. (relative amounts of each different molecular structure). Reaction modelling usually uses energetics to decide relative likelihood of following different reaction pathways. The computational resources required for such models are large. I wish to shortcut that by using RELATIVE rate parameters for the various types of C-N bond formations. I want to supply to the model: * an integer value for the number of molecules of ammonia and/or each type of preformed ethyleneamine, * an integer value for the number of molecules of EDC, * rules for what new bonds can be formed [determines the possible structures of the final products]... and... * adjustable relative rate parameters for each type of displacement reaction. I would limit these to six [ammonia/EDC, primary NH2/EDC, secondary NH/EDC, secondary cyclic NH/EDC, intramolecular primary NH2 and intramolecular secondary NH]. Rather than supplying the reaction pathways and product structures. I want to avoid this 'exhausting enumeration' with a program that keeps track of which new bonds are formed, determines the product structure and represents it graphically (e.g.- CH2-CH2 / \ HN NH \ / CH2-CH2 ) [original in monospaced font] for piperazine, a common lower product of this reaction. Does anyone know if such a model already exists or that there are the pieces to build it? Sincerely, Forrest Richey far@medinah.atc.ucarb.com From richard@iris26.biosym.com Thu Sep 16 02:46:14 1993 Message-Id: <9309161646.AA09482@iris26.biosym.com> To: chemistry@ccl.net Subject: Distance Geometry program Date: Thu, 16 Sep 93 09:46:14 -0700 From: Richard Macdonald To answer the person's question about Tim Havel's DGII program: DGII has been incorporated into Biosym's Insight II software and can be used by the NMR refinement module in the current release, and also in the Homology module in the forthcoming release. ---> richard *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 *********************************************************** From adit@Kodak.COM Thu Sep 16 09:10:57 1993 Date: Thu, 16 Sep 93 13:10:57 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9309161710.AA00470@bcc9.kodak.com> To: chemistry@ccl.net Subject: posters on workstations? POSTERS ON WORKSTATIONS. SUMMARY I would like to explore with you my observations about traditional poster sessions at computational meetings and to suggest a new way of organizing them that will be more profitable to all of the participants. If the responses are positive and the application rate high enough I am ready to organize this at the next MM/MD workshop in Tallahassee next Feb.Your helpful comments, and participation in this event would be valuable. BACKGROUND I have often been at computational meetings where the poster session consisted of "white boards" to which the participants pinned 2D pictures and other representations of their work. Almost without fail the discussions are peppered with the statements like "This picture just doesn't show the correct angle but if I could just rotate it..." Or "If you can simply imagine the other possible low energy conformation where !@#$ is flipped..." etc. The point is that the work we do is **INHERENTLY** 3 dimensional and we are trying to represent it (in limited physical space) in two dimensions. Often not more than a few feet away are some of the same types of workstations that the work was generated on, running some of the same types of software that the work was generated with. And these folks are hungering for "real" examples of the use of their product. Well, by now you see where I am headed... Wouldn't it be nice if the posters could be run INTERACTIVELY on the workstations! (Is this a "novel" idea or has it been done already?). The whole thing seems like a "win-win situation" to me. The poster participants get to show and see the ACTUAL results of the experiment. Further they get to ask computational questions RIGHT ON THE SPOT and get answers just as fast. Of course the participants get to benefit because for the first time (even journal articles can't expose the work to the same level of scrutiny and input from the community) they can benefit from the combined wisdom of all of their community members.Questions about running of the same type of experiment in DIFFERENT packages can be answered on the spot too. The vendors will have their long sought after "real" examples put forward by people who are REALLY using the programs for their daily work showing it to people who may be interested as much in the software as in the SCIENCE of what is being shown. The dream of having users of the software "sell" other users on the use of the programs may actually come true. PROPPOSAL: Through the kindness and diligence of others I have reason to believe that many (if not most) of the major vendors of computational software are willing to support this venture at the next MM/MD Workshop in Tallahassee in late February 1994. If you are interested in participating contact Del Detar at the address shown below or contact me (I am on the organizing committee too) If you are interested in participating in this electronic poster session please indicate the software/hardware that you would prefer to present on. This will enable me to firm commitments with the software vendors. Detar, Delos F. 1912 Sharon Rd. Dept. Of Chem. FSU Tallahassee, FL. 32303 (904)644-3709 FAX (904)644-8281 DETAR@FSU.bitnet You would work out the software/hardware platform that you would need and if it was available you would simply bring a tape to the meeting, load it on the assigned machine at the assigned time and you would then be ready to interact with your data to show it to your interested colleagues. If there is a large demand and a limited supply of platform combinations then some sort of time sharing will have to be done at this first trial of the approach to posters. I would value input from EVERYONE who cares as I would like to make this something that we would all remember as a computational community event. Thanks in advance for your help. Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com From jaeric@mtcamm.monsanto.com Thu Sep 16 10:42:26 1993 From: Jon A. Erickson Message-Id: <9309162042.AA05475@mtcamm.monsanto.com> Subject: Re: NH3/Dichloroethane > Ethyleneamines Model To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Thu, 16 Sep 93 15:42:26 CDT > I'm looking for a computational model of the reaction of ammonia with > 1,2-dichloroethane. That is C-N bond formation between ammonia (and > resulting intermediate amines) and 1,2-dichloroethane (EDC). The > products, commonly known as ethyleneamines, contain a great number of > homologs and isomers. > > What I want from the model is a product distribution. (relative amounts of > each different molecular structure). > > Reaction modelling usually uses energetics to decide relative likelihood of > following different reaction pathways. The computational resources > required for such models are large. > I think the CAMEO program from Jorgensen's group is the closest thing to what you want. See J. Org. Chem 55 (1990) 9 and contact cameo@doctor.chem.yale.edu. -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. FAX: (314) 694-1080 # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From gford@sgi1.chem.smu.edu Thu Sep 16 10:31:00 1993 Message-Id: Date: Thu, 16 Sep 93 17:31 PDT From: gford@sgi1.chem.smu.edu (George P. Ford) To: chemistry@ccl.net Subject: Gibbs free energy of solvation Original message .... >Dear mailers, > >I am interested in the Gibbs free (or Helmholtz) energy of the >following process: > > MCl (vac) ----> MCl (aq) > DG > >M represents a charged molecule (say serotoninH+). Cl is an arbitrary >couter ion. DG must contain the change in Gibbs free energy of the >complex as well as that of the water. >Does anybody know of a simple and quick way to estimate DG (and >references in literature)? I am specially interested in methods using >(functional) group contributions, but other methods may be interesting >as well. > >Best regards, > >Marcel Verdonk, >Dept. of Crystal and Structural Chemistry, >Utrecht University, >Padualaan 8, >3584 CH UTRECHT, >THE NETHERLANDS. Dear Marcel: Of the publicly available methods for estimating hydration energies of organic ions you would probably get the results using AMSOL [1]. This is available through QCPE and is also included in AMPAC. Although other methods do better for the electrostatic parts (both ours [2] and COSMO [3]) these include no way to allow for non-electrostatic contributions. Warren Hehre's method, incorporated in SPARTAN, is very good and is much more stable than AMSOL but has yet to be parameterized for ions and is so far unpublished. The only way of estimating hydration energies of ions using functional group contributions I know of is one we published some time ago [4]. This was essentially an extension of Hine and Mookerjee's work on neutral molecules. We derived new contributions for charged groups and added an electrostatic term based on a simple two-shell Born model. In actual use the neutral group contributions suggested by Cabani et al [5] are easier to use and more versatile use than Hine's. The method works best for molecules that are approximately spherical and where there is little conjugative interaction. Yours is therefore not an ideal case. With this in mind, the hydration energy given by this simple additivity method (concentration based standard states) for the serotonin conjugate acid is 75.8 kcal/mol. This can be compared with the SM2 result (AMSOL) of 77.6 kcal/mol obtained by making the simplifying assumption that the aqueous-phase geometry is the same as the gas-phase one (without this assumption you will consume an awful lot of computer time and not necessarily get a better answer). If you are interested in the additivity method email me directly and I'll get the necessary tables to you together with a line-by-line explanation of how I got the estimate above for serotoninH+. [1] C. C. Cramer and D. G. Truhlar, J. Computer Aided Mol. Design, 1992, 6, 629-666 and earlier papers. [2] G. P. Ford and B. Wang, J. Am. Chem. Soc., 1992, 114, 10563-10569. This method has now been improved through the use of a new model quantum mechanical potential (G. P. Ford and B. Wang, J. Comput. Chem., 1993, 14, 1101-1111). An ms is in preparation. [3] A. Klamt and G. Schuurmann, Perkin Trans. 2, 1993, 799-805; available in MOPAC7 and MOPAC93. [4] G. P. Ford and J. D. Scribner, J. Org. Chem., 1983, 48, 2226-2233. The supplementary data to this paper includes tables that permit simple "pencil and paper" hydration energy estimates. [5] S. Cabani, et al, J. Solution Chem., 1981, 10, 563-595. =========================================================================== George P. Ford | email: gford@sgi1.chem.smu.edu Department of Chemistry | voice: (214) 768-2479 Southern Methodist University | fax: (214) 768-4089 Dallas, Texas 75275 | =========================================================================== From d3g681@fermi.pnl.gov Thu Sep 16 12:23:35 1993 Date: Thu, 16 Sep 93 19:23:35 -0700 From: Robert J Harrison Subject: Parallel chemistry code development To: CHEMISTRY@ccl.net Message-Id: <9309170223.AA06898@fermi.pnl.gov> Replies directly to rj_harrison@pnl.gov. I'd be interested in hearing from people developing parallel chemistry codes - what is your application ? - what programming environments/tools are you using ? - what do you think about available tools ? - what platforms will you be running on ? If there is sufficient response, I shall post a summary. Robert J. Harrison Mail Stop K1-90 tel: 509-375-2037 Battelle Pacific Northwest Laboratory fax: 509-375-6631 P.O. Box 999, Richland WA 99352 E-mail: rj_harrison@pnl.gov