From chemistry-request@ccl.net Tue Mar 24 06:23:01 1992 Date: Tue, 24 Mar 92 10:12:42 PRT From: Dionisia Maria de Jesus Subject: Reply to my queries about Postgraduate To: CHEMISTRY@ccl.net Status: R To my queries here are some reply Many thanks to the persons who reply. Dionisia Maria de Jesus ========================================================================= Date: Thu, 19 Mar 1992 19:57:35 EST From: breneman@XRAY.CHEM.RPI.EDU To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: RE: Hi Postgraduate info From: Dan Severance Subject: Re: Hi Postgraduate info To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU (Dionisia Maria de Jesus) Date: Thu, 19 Mar 92 18:11:09 EST Organization: Laboratory for Computational Chemistry Date: 19-MAR-1992 18:18:50.39 From: WSONNEN@EAGLE.WESLEYAN.EDU Subject: postgraduate studies To: sceioc23%ptearn.bitnet@cunyvm.cuny.edu Date: Fri, 20 Mar 1992 09:55 EST From: "To help us serve you better, please take a number..." Subject: Re: Hi Postgraduate info To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Date: Fri, 20 Mar 92 15:21:43 -0800 From: yee@gold.cchem.berkeley.edu (Raymond Yee) To: CHEMISTRY@ccl.net, SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Re: Hi Postgraduate info Date: Fri, 20 Mar 92 09:59:07 JST From: osawa@cochem.tutkie.tut.ac.jp (Eiji Osawa) To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Re: A possibility of postgraduate study Date: Fri, 20 Mar 92 16:10 EST From: COFFEE DRINKERS MAKE GOOD LOVERS Subject: Re: Hi Postgraduate info To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Date: 20-MAR-1992 11:34:12.75 From: Joe Ochterski Subject: Re: Hi Postgraduate info To: SCEIOC23%PTEARN.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Organization: Wesleyan University Chemistry Dept. Date: Tue, 24 Mar 92 09:40:05 EST From: GWA@CU.NIH.GOV Subject: New Journal of Molecular Modeling To: chemistry@ccl.net Status: R There is a proposal before the ACS to begin a Journal of Molecular Modeling. This journal could deal with theory or applications, or both. What is your reaction to this? Good idea? Bad idea? No need? Thanks, Bill Milne From chemistry-request@ccl.net Tue Mar 24 11:21:42 1992 Date: Tue, 24 Mar 1992 09:46 EST From: "DOUGLAS A. SMITH" Subject: ab initio of organometallics To: chemistry@ccl.net Status: R Given all of the various prejudices concerning theoretical methods, this may be opening a can of worms - but it should make for some interesting discussion as well. What is the preferred method for ab initio (not semiempirical or DFT) calculations on organometallic compounds, including both group IA and IIA and transition metal species? I know basis sets become a real problem for some metals, and the LANL bases are mimimal on the organics, so that a rigorous theoretical method may far exceed the capabilities of your basis set (this doesn't even get into the question of effective core potentials). When I say best, I am asking for opinions as to the most effective, efficient, least costly, most accurate, etc. Is GVB better than HF, or is CI or CC required? Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From chemistry-request@ccl.net Tue Mar 24 14:24:08 1992 Date: Tue, 24 Mar 92 10:11:58 PST From: crc@iris12.biosym.COM (Clifford Randall Cannon) Subject: About Bill Milne's note, proposed ACS Journal of Molecular Modeling. To: chemistry@ccl.net Status: R There is already an (international) Molecular Graphics Society, with an affiliated Molecular Graphics Society of the Americas (members from both North and South America) and a quarterly journal. The MGS is basically a modeling organization, not just graphics, and they are considering changing the name to reflect that. Probably some coordination between ACS and MGS would save duplicated efforts (unless some big egos are involved, in which case there will be no shortage of energy--heat, at least). From chemistry-request@ccl.net Tue Mar 24 14:24:15 1992 Date: Tue, 24 Mar 92 16:33:26 GMT From: Chris Plant Subject: lost paper To: chemistry@ccl.net Status: R Hello, I've never quite seen the list used for the following before, but I might as well give it a shot... We had a paper accepted for publication by the Structural Chemistry journal (Eds: Art Greenberg & Istvan Hargittai) sometime around late spring of last year, but haven't seen any sight of it since. The paper is entitled something like "Rotational Barrier Heights in Ethene Thiol: An ab initio study" ... its been so long I can't quite remember the exact title! The authors are C.Plant, J.E.Boggs, G.A.Williams, & J.N.Macdonald. I do not have access to an appropriate library here, so my questions are as follows; 1) If anyone has ready access to this journal and has seen the paper (it really "should" be out by now), can you let me know the reference please as we need it for a grant proposal. 2) If no one has seen the paper, can someone tell me an e-mail address for Art Greenberg (Rutgers, NJ) so I can press him for more details. Thanks in advance for any assistance. Chris Plant Scientific Applications Support Atlas Centre Rutherford Appleton Labs (UK). email cp5@ib.rl.ac.uk From chemistry-request@ccl.net Tue Mar 24 15:44:30 1992 Date: Tue, 24 Mar 92 13:50:02 -0500 From: fredvc@esvax.dnet.dupont.COM Subject: RE: New Journal of Molecular Modeling To: "gwa@cu.nih.gov"@esds01.dnet.dupont.COM Status: R I think that such a new journal would be a bad idea! (1) From a purely selfish perspective, the last thing I need is yet another journal to keep up with. Things are tough enough as it is!! There are a number of journals already that are appropriate venues for publication of work of the type outlined. (3) Molecular modeling is not a field unto itself. We carry out modeling to gain insight into chemistry, physics, biochemistry, biology, etc. I am opposed to anything that takes it out of the proper context. I hope that no one does modeling for its own sake. This would seem to me to be a sterile endeavor. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 Central Research & Development Dept. || FAX: (302) 695-9658 The Du Pont company || P. O. Box 80320 || Internet: fredvc@esvax.dnet.dupont.com Wiilmington DE 19880-0320 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From jkl@ccl.net Tue Mar 24 16:02:49 1992 Date: Tue, 24 Mar 1992 16:02:41 -0500 From: jkl@ccl.net To: chemistry@ccl.net Subject: RE: New Journal of Molecular Modeling Status: R Forwarding to the list: ---------- Begin Forwarded Message ---------- Date: Tue, 24 Mar 1992 15:46:27 EST From: FAERMAN@BRIMV.BRI.NRC.CA Subject: RE: New Journal of Molecular Modeling To: chemistry-request@ccl.net I believe it is not a very good idea since there are many Journals that do publish material in this field. Furthermore, the trend seems to be towards a larger and yet larger number of Journals as opposed to improving the quality of the existing ones. Having in mind the tight budgets we all have it would be difficult to convince the Funding Agencies to buy Journals that are not yet well known. This points to the general issue of the audience You would like to address. ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Tue Mar 24 17:07:33 1992 Date: Tue, 24 Mar 92 13:07:23 -0800 From: ross@zeno.mmwb.ucsf.EDU (Bill Ross) Subject: journals To: chemistry@ccl.net Status: R A refereed journal on the net would get my vote. An old one converting would be preferable, but I suspect it may take a new one to get over the hump. (I am aware there is a Mac disk journal.) While on the subject, a wonderful intermediate exists in the newsgroup bionet.journals.contents, each posting on which contains a table of contents in bib-style reference form for a volume or issue of a journal. If it only could include more general chemistry etc journals.. Credit to Dave Kristofferson at GenBank for this handy newsgroup. Bill Ross From chemistry-request@ccl.net Tue Mar 24 17:31:22 1992 Date: Tue, 24 Mar 92 13:26:52 EST From: Mark Murcko Subject: Re: New Journal of Molecular Modeling To: GWA@cu.nih.GOV, chemistry@ccl.net Status: R What is the difference between the Journal of Computational Chemistry, the Journal of Molecular Graphics, Computers in Chemistry, PROTEINS, THEOCHEM, J. Biomol. Struc. & Dynamics, Macromolecules, Biopolymers, etc? Of course, some of these journals have obviously different slants, but the point is that molecular modeling is *used in* and is a *part of* many different disciplines and kinds of study. Given the current existence of so many other "modeling" type journals, do we really need another? / Mark (markm@vpharm.com) From chemistry-request@ccl.net Tue Mar 24 19:21:10 1992 Date: Tue, 24 Mar 92 14:22:58 PST From: whitbeck@wheeler.wrc.unr.EDU (Mike Whitbeck) Subject: Re: journals To: chemistry@ccl.net Status: R Bill Ross says..."A refereed journal on the net would get my vote." I think there are some philosophical barriers to a refereed journal via the net but it certainly should be feasible. Technically it would require the adoption of a standard display language such as postscript. [Is color postscript well established? ] I presume that Mac's and PC's can view postscript via some filter like ghostscript. The main difficulty is in getting editors who can put in the time. Accepted articles need not be typeset in a journal like fashion but that would add extra value to the 'journal', as would an index, table of contents, back issues... This would require the adoption of a mark-up language or program. As far as I know TeX and perhaps WP are the only document prep languages widely available on most of the computers in use (Mac, PC, UNIX, etc.). [there may be incompatibilities between WP on different platforms...I'm not sure] But could such a journal be cited in refernces? Would it have a wide enough distribution to have any meaning as a publication in the current sense of the word? I am at my limit on personal subscriptions and I'm sure libraries are equally hard pressed to come up with money for ever-more-specialist journals. A journal distributed over the net would appeal to me on several levels: (1) no paper clutter unless I snip and print those pages of interest (2) electronically searcable (perhaps) for keywords (3) inexpensive (hopefully) BUT such a journal would be worthless unless it is well and faithfully produced and articles are subjected to the highest standards of review. -- Mike Whitbeck From chemistry-request@ccl.net Tue Mar 24 20:10:35 1992 Date: Tue, 24 Mar 1992 17:36 CST From: CMSWALTERS@minna.iit.EDU Subject: magnesium To: chemistry@ccl.net Status: R Hi Netters, I'm looking for two things today: 1. Parameters and/or exciting stories about modeling Mg++ in proteins. I prefer charmm parameters, but if params are really scarce, who knows? 2. Info on molecular volumes of the standard amino acids; this could be a source of the data in literature or a cheap/public domain program to calculate them. I have a file folder full of papers dealing with partition coeffs of amino acids but can't find volumes... Thanks for your help! Eric Walters >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > D. Eric Walters > > Assoc. Prof. Biological Chemistry > > Chicago Medical School phone: 708-578-3000, ext 498 > > 3333 Green Bay Road fax: 708-578-3240 > > North Chicago, IL 60064 email: cmswalters@minna.iit.edu > > > > "We have no money, therefore we must think" --Sir Ernest Rutherford > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From chemistry-request@ccl.net Tue Mar 24 20:16:38 1992 Date: Tue, 24 Mar 1992 18:57 EST From: LAVRENTYEV@rcgl1.eng.ohio-state.EDU To: chemistry@ccl.net Status: R I've recieved from Russia an advertisment of a new chemical process. It may be interesting for the list subscribers. Sincerely, Anton. ******************************************************************* ECOLOGICALLY PURE METAL SAVING WASTELESS CHEMICAL PROCESSES _________________________________________________________________ Igor P.Lavrentiev, Head of Laboratory. The Institute of Chemical Physics in Chernogolovka, Russian Academy of Sciences 142432, Chernogolovka, Moscow Region, RUSSIA (USSR) Phone: 524-50-87 , 524-50-35 (Moscow); Telex: 412652 KLEN SU; E.mail: lip@imm.sherna.msk.su or ngm@kiae.su (for I.P.Lavrentiev) The fundamental research of the reactivity of metals and oxides in organic and aqueous-organic media is used in the development of selective low metal-and raw material-intensive wasteless (or low-waste) ecologically pure technologies. The results may be applied to electronics, chemical and metallurgical industries and in the processing of primary and secondary raw materials. I. Selective Extraction and Synthesis. - Selective extraction of noble metals (gold, silver, platinum, palladium, rhodium and etc.) from various sources. The method can be applied to the processing of solid products metals from secondary raw materials: various waste catalysts, including, reforming process, vinyl acetate production, "neutralizers" of exhaust gases of motor transport, contacts of radio ware, jewelry, primary and secondary raw materials, including waste nuclear fuel,.and communications and industrial reactors. - Selective Etching (Dissolution) of Metal and Oxide Materials and Coatings of Various Origin. The method may be used, in for the wasteless production of printed circuit boards, in the chemical and mechanic-chemical polishing of glasses and other oxide materials including semi-precious and in optics. - Regeneration of Metal Platinoid Catalyst ("Net") The method is based on the selective extraction of catalytic poisons and other impurities, which isolate the catalyst surface, without the surface destruction and loss of noble metals. - Regeneration of Au-, Ag-, Pd-, Rh-, Ru-, Ir-, Re- and Pt - containing Deposited Heterogeneous Catalyst. The method is based on the selective extraction of catalytic poisons isolating the catalyst surface and realization of Redox processes on the surface to modify the catalytic active centers. - Regeneration of the Magnetic Discs Bases. The method is based on the selective extraction of iron oxide from the polymer matrix (ferrilaquer) or dissolution (stripping) of ferrilaquer with the retention of the structure and quality of the disc base surface. - Purification of Plated Metal Surfaces. The method is based on the selective extraction of metals and their compounds (oxides, carbides, and carbon) from the surface of metallated wares without disturbance of its structure and quality. The method also provides the possibility of purification of other metal surfaces, e.g.of internal-combustion engines and diesels, of wasted sparking plugs, of guns and other articles. - Purification of Free Elements and their Compounds (oxides, nitrides, borides, etc.) The method is based on the selective extraction of metals and their compounds from starting materials. - Processing of copper-containing raw source. The method may be applied to the production of powder of metallic copper when extracting from liquid and solid waste materials, including the preparation of highly purified ultradisperced copper powder (0,5-2 mm) - Direct synthesis of coordination compounds. The method may by applied to the obtaining of metal complexes by a direct single-stage process. II. Controlled Deposition. - Controlled deposition of copper, silver, gold, palladium, platinum, rhodium and other metals including coatings of a film type. The method can be used for the metal deposition to various surfaces (adsorbents, metals, plastic materials, wood and etc.) for the synthesis of deposited heterogeneous metallic catalysts (e.g., "neutralizers" of exhaust gases of motor transport), to form multilayer film coatings, including those on badly accessible surfaces, for the foil and ultradisperced powders production and in the art and technology of jewelry. - Production of Metal (Cu, Fe,Mn and etc.) Oxide in liquid phase,Catalysts and coatings on their Base and other oxide - containing materials. The method can be used for the development of single - stage wasteless technology of oxides production (CuO, Fe O , g-Fe O , MnO and etc.), complex oxide systems (film-like as well), for the production of oxide deposited catalysts e.g., "neutralizers" of exhaust gases operation of industrial energy installations, and for the chromophores preparation in the dyes production. _________________________________________________________________ From chemistry-request@ccl.net Tue Mar 24 23:53:20 1992 Date: Wed, 25 Mar 1992 13:09:09 +1000 From: apa@ccadfa.cc.adfa.oz.AU (Alan P Arnold) Subject: *Help* with Thermodynamic Integration, please... To: chemistry@ccl.net Status: R To all practitioners of the black art of Thermodynamic Integration, (and devotees of 'slow growth' and Free Energy Perturbation) ... Greetings, in an effort to generate some discussion about molecular dynamics methodology for calculating free-energies (and so that I might increase my scant knowledge), I offer the following data based on a tutorial on 'relative free energy' in Biosym's Discover manual - "Performing a Methanol to Ethane Free Energy Calculation". I have performed the aforementioned gas-phase calculation, in which one molecule of methanol is alchemically 'warped' into a molecule of ethane. Biosym's cvff forcefield was used, and the free-energy change was calculated by Thermodynamic Integration with 6 quadrature points, dlambda=0.005. The example in the manual used 10,000 x 1fs (=10ps) equilibration, followed by 10,000 x 1fs (=10ps) dynamics at 300K and the free-energy change is reported as 1.45 +/- 0.19 kcal/mol. After installation of our new version of Discover, I performed this calculation, giving a free-energy change of -0.98 +/- 0.15 kcal/mol. I was worried that this difference was due to the change to the new version of Discover (2.08b) but then realised that the initial velocities are randomised with different seeds. Even so, the difference between these two numbers was intriguing, so I did a few more runs (identical integration parameters) which are summarised below. run# stepsize/fs equil.steps dynamics steps dA +/- 0 1.0 10,000 10,000 +1.45 0.19 (tutorial) 1 1.0 10,000 10,000 -0.98 0.15 2 1.0 10,000 10,000 +0.67 0.22 .. "obviously" (?!) equilibrium not reached, so 3 1.0 20,000 10,000 +1.24 0.19 4 1.0 20,000 10,000 +1.51 0.18 .. Ah, much better, but let's try to get those std.devs smaller! 5 1.0 20,000 20,000 +0.53 0.17 6 1.0 20,000 20,000 -0.43 0.12 .. Maybe the steps are too big for such small molecules :-) 7 0.5 20,000 20,000 +0.93 0.17 8 0.5 20,000 20,000 +1.75 0.16 I have plotted Temp (and E_Total and E_Potential) vs time for several of these runs (during both the equilibrium and dynamics phases, for each of the lambda steps) and am worried by the wide temperature variation. For example, run 1: lambda Temp. +/- E_Tot +/- E_Pot +/- 0.05635 299.9 7.0 23.03 1.53 15.88 1.54 <- equm phase 300.0 7.7 22.08 0.03 14.92 0.18 <- dynamics phase 0.20000 299.9 7.4 22.96 0.82 15.81 0.84 299.6 23.7 24.28 0.41 17.14 0.69 0.44365 299.9 10.2 26.81 0.91 19.66 0.96 300.3 36.5 27.21 0.45 20.05 0.88 0.55635 299.9 10.0 25.84 1.28 18.69 1.29 300.0 38.3 26.02 0.21 18.87 0.92 0.75000 299.8 11.0 26.55 1.26 19.40 1.28 300.2 50.2 26.36 0.30 19.21 1.19 0.94365 299.9 8.6 25.37 0.61 18.22 0.63 300.4 49.3 25.44 0.22 18.28 1.16 At this stage I realised that I don't really understand what is going on here and such powerful tools are dangerous in the hands of incompetents. A few questions: 1) What steps must one take to ensure that more than two successive runs will give agreement within a few +/-'s? I conclude that agreement between runs 0,3&4 is fortuitous. Simply making the run longer doesn't seem to be the answer (see runs 5&6 cf 3&4). 2) What about the temperature (and energy variations) - is this normal? 3) Is the number of quadrature points a problem? If so, how do you choose the correct number? 4) What about d(lambda)=0.005? Too small, too big? How do you know? 5) How do you make the +/-'s smaller? My apologies for the length of the posting, but I think that many of us would appreciate pointers to pitfalls in this area, by some of you who are more expert. * All* comments are very welcome (by e-mail if they are abusive!). Thanks for listening, Alan Arnold | e-mail: apa@ccadfa.cc.adfa.oz.auChem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2600 Australia | PS my apologies to the administrator/s of this discussion group -\ for sending a copy to chemistry-request rather than chemistry!