From DSMITH@uoft02.utoledo.edu Mon May 17 04:21:11 1993 Date: Mon, 17 May 1993 09:21:11 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: semi.QM energy of electron/proton?? To: moret@far.ruu.nl Message-Id: <01GY9Z3W7O1A0090QS@UOFT02.UTOLEDO.EDU> In regards to the semiempirical energies (more correctly, heats of formation) of the proton and the electron, I seem to recall a value of around 310 kcal/ mol for a proton. However, I ran the simple, single point calculation (using HyperChem) of H+ with the AM1 parameters and get a value of 262.8032. You should try this with MOPAC 6 (I would, but I am sitting at my PC so Hyperchem, not MOPAC, is readily available). I cannot do the same for a single electron with Hyperchem. Try using MOPAC, define a dummy atom, set the charge on the system equal to -1 and the multiplicity as a doublet, and see what happens. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From toni@athe.wustl.edu Mon May 17 06:28:55 1993 Date: Mon, 17 May 93 11:28:55 CDT From: toni@athe.wustl.edu (Toni Kazic) Message-Id: <9305171628.AA13853@athe.ibc> To: richard@technology.com Subject: help needed Walter, I am working on biochemical and physiological kinetics, so this may be only marginally relevant to you. We have worked so far on essentially only representations, not stocking the database with lots of facts. 1. Name: Toni Kazic 2. Company: Institute for Biomedical Computing, Washington University 3. Telephone number: 314-362-3121 3.a E-mail: toni@athe.wustl.edu 4. Chemical kinetics application: biochemical database 5. Are the rate coefficients you use a. in Arrhenius form: A~(T/To)B~exp(-C/T)? b. in another form? (Please specify): enzymological constants as in the literature (these are quasi-standardized) 6. Does your database contain references for the source of the coefficients? Yes 7. What is the maximum number of reactants (including catalysts) in a reaction? No limit 8. What is the maximum number of products (including catalysts) in a reaction? No limit 9. Please attach a very short sample printout of your database (we just want to know the FORTRAN format). Not FORTRAN, Prolog. I can send you the separate Prolog facts or a PostScript pretty printout. From richard@TC.Cornell.EDU Mon May 17 08:31:18 1993 Date: Mon, 17 May 1993 12:31:18 -0400 From: Richard Gillilan Message-Id: <199305171631.AA00276@theory.TC.Cornell.EDU> To: chemistry@ccl.net Subject: analysis of diffaction data Is anybody out there familiar with the program MOSCO (part of ccp4 from Darsbury)? Where can I get information about it? Is source code available and at what cost? Are there any other similar codes that are better? Thanks ------------------------------------------------------------------- stereo pair stereo pair Richard E. Gillilan H H H H Visualization Specialist \ | | \ Cornell Theory Center H--C---C--H H---C---C---H richard@tc.cornell.edu / | | / (607) 254-8757 H H H H ------------------------------------------------------------------- From jle@world.std.com Mon May 17 10:30:42 1993 Date: Mon, 17 May 1993 14:30:42 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199305171830.AA05935@world.std.com> To: chemistry@ccl.net Subject: Seeking octanol data... Folks, I'm interested in getting a reference or three containing either solvation data for stuff in octanol, or better, delta-G solvation of stuff in octanol. Anybody with a pointer would be appreciated - this is for a cohort w/o net access... Joe Leonard jle@world.std.com From mail Mon May 17 14:03:05 1993 Date: Mon, 17 May 1993 13:56:52 -0400 From: hyper!guo (Yufei Guo) Message-Id: <9305171756.AA14728@hyper.hyper.com> To: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" , Subject: Re: semi.QM energy of electron/proton?? Hi Dr. Smith, I think you mis-interpreted a HyperChem result in your recent email to the OSC exploder. You wrote: > In regards to the semiempirical energies (more correctly, heats of formation) > of the proton and the electron, I seem to recall a value of around 310 kcal/ > mol for a proton. However, I ran the simple, single point calculation > (using HyperChem) of H+ with the AM1 parameters and get a value of > 262.8032. You should try this with MOPAC 6 (I would, but I am sitting at > my PC so Hyperchem, not MOPAC, is readily available). I have run the calculation with HyperChem and MOPAC 6.0. Both give the same answer for the heat of formation for H+ of 314.9 kcal/mol. The number of 262.8032 that you got (presumably from the status line) is the *binding* energy, not the heat of formation (which is in the log file or available via script or DDE). The binding energy is the total system energy minus the sum of the energies of the isolated atoms (not ions), which in this case is the difference in energy between the hydrogen atom and cation. > Doug > > Douglas A. Smith > Assistant Professor of Chemistry > The University of Toledo > Toledo, OH 43606-3390 > > voice 419-537-2116 > fax 419-537-4033 > email dsmith@uoft02.utoledo.edu Hope this helps, Yufei Guo From raman@bioc01.uthscsa.edu Mon May 17 13:22:16 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305172322.AA14653@bioc01.uthscsa.edu> Subject: Octanol To: chemistry@ccl.net Date: Mon, 17 May 1993 18:22:16 -0500 (CDT) > either solvation data for stuff in octanol, or better, delta-G > solvation of stuff in octanol. Anybody with a pointer would be > appreciated - this is for a cohort w/o net access... > What is "stuff" supposed to mean here? I can give you citations for free energies of transfer in Octanol and Water for various amino acids. That work appeared in the early '70s by Nozaki and Tanford. The papers were in the Journal of Biological Chemistry. If this is what you are looking for let me know and I can include other references as well. -- 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 craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From aes@stan.xx.swin.OZ.AU Tue May 18 07:20:33 1993 From: aes@stan.xx.swin.OZ.AU (LOHNING A) Message-Id: <9305180220.AA24196@stan.xx.swin.OZ.AU> Subject: MOPAC6.0/Selenium To: CHEMISTRY@ccl.net Date: Tue, 18 May 93 12:20:33 EST Dear Chemnetters, I am trying to do some molecular orbital calculations (using MOPAC 6.0 & PM3 parameters) on a selenium-containing amino acid residue. For some reason there's a problem accessing the new Selenium parameters. I was wondering if anyone else is working with selenium in this context and/or could suggest a course of action for me. I would greatly appreciate any help at all & thank you in advance. Anna Salinas C/- Chemistry Department Swinburne University of Technology John Street Hawthorn 3123 Victoria Australia Tel: (03) 819 8911 E-mail: aes@stan.xx.swin.oz.au From raman@bioc01.uthscsa.edu Mon May 17 17:39:21 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305180339.AA14702@bioc01.uthscsa.edu> Subject: Re: Seeking octanol data... To: jle@world.std.com (Joe M Leonard) Date: Mon, 17 May 1993 22:39:21 -0500 (CDT) Joe, Here are some of the recent references in this area that might help you: 1. Pharmaceutical Research [1992] 09,504-514 "Amino acid side chain contributions to the free energy of transfer of tripeptides from water to Octanol" 2. Thermochimica Acta [1989] 152, 463 Thermodynamic titration method for the estimation of energetics of transfer of very lipophilic solutes from water to Octanol" 3. Biochemistry [1991] 30, 9686 "Extracting free energies from transfer data 4. J. Phys. Soc. Jpn. [1991] 60, 2783 "Hydration thermodynamics of Biomolecules: transfer free energies of amino acid and derivatives" 5. ibid. [1991] 60, 330 " similar title ....... " The Original Nozaki and Tanford papers: a. J. Biol. Chem. [1971] 246, 2211 b. ibid. [1970] 245, 1648 You should have no trouble finding additional citations from the bibliography provided by the above mentioned references! Hope this helps! -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 craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ******************************************************************************