From owner-hyperchem@hyper.com Mon May 1 17:14:53 1995 Date: Mon, 1 May 95 12:49:05 -0400 From: polowin (Joel Polowin) To: dsmith@doane.edu Subject: Re: wierd printing Cc: hyperchem > From: dsmith@doane.edu > Date: Fri, 28 Apr 1995 14:16:50 -0500 > > When we draw a molecule, add H and model build, and render it in spheres, it > will print ok the first time. Thereafter, the molecule is split into 3 parts. > For instance, on the second printing the molecule should be 70 mm in length, > but the top 6 mm are cut off and printed on the *bottom*, and the bottom 6 mm > are printed on the top. The two fragments are printed about 13 mm from the > bulk of the molecule. Subsequent attempts to print get worse--on the fourth > printing the molecule is divided into thirds. > > If we clear out this molecule and draw a new one, the cycle begins again--a > good first printing... There's a known bug in Release 2 of HyperChem that would cause rendered spheres to come out in inverted strips on some printers, but that doesn't sound like what you've got, exactly. (This problem was fixed in Release 3, I believe; as far as I know the effect was consistent and couldn't be fixed even temporarily.) It sounds like something in the output process is getting confused with regard to the setup of the page. If this were a dot-matrix printer, I'd be thinking that either the printer driver or the printer itself had been misinformed about the number of lines per page, or the top and bottom margin size -- something like that. A laser printer should be processing the picture in a graphics format that shouldn't be affected by the page setup in quite the same way. Still, that's the sort of thing I'd be looking for: check the printer, to see how it's configured for margins and lines per page; check the printer driver to make sure that it's set for the right kind of paper and to see if it has configurable options like the above. What kind of printer are you using? Is any other software giving you oddly-formatted output when you send it to that printer? Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From 91230268@vax1.dcu.ie Thu May 4 15:52:59 1995 Date: Thu, 04 May 1995 14:31:04 +0000 (GMT) From: NAZGUL <91230268@vax1.dcu.ie> Subject: Question To: hyperchem@hyper.com I've recently started using Hyperchem/Chem+ and I'm having problems with the Conformational Search option. I'm modelling calix[4]arenes (four benzene rings in a cyclic array, linked by CH2 groups in the meta position). Whenever I select a torsion involving the carbon of the CH2 group and a benzene ring and run the Search I get error messages refering to not being able to cope with acyclic torsions, but I need to vary these torsional angles. Does anyone out there have any suggestions??? Thanks in advance, Darren Fayne ________________________________________________________________________ From owner-hyperchem@hyper.com Thu May 4 21:06:31 1995 Date: Thu, 4 May 95 16:29:49 -0400 From: polowin (Joel Polowin) To: hyperchem Subject: Re: Question > Date: Thu, 04 May 1995 14:31:04 +0000 (GMT) > From: NAZGUL <91230268@vax1.dcu.ie> > Subject: Question Hi, Darren. > I've recently started using Hyperchem/Chem+ and I'm having problems > with the Conformational Search option. I'm modelling calix[4]arenes (four > benzene rings in a cyclic array, linked by CH2 groups in the meta position). > Whenever I select a torsion involving the carbon of the CH2 group and a > benzene ring and run the Search I get error messages refering to not being > able to cope with acyclic torsions, but I need to vary these torsional angles. I'm afraid that I can't visualize what angles you're trying to set here. It sounds like you're working on the same sort of problem as Paddy Kane described at the end of March. Here's what he asked, and my reply to him: ---------- > I wish to know how to rotate a benzene ring andany groups attached through > an angle of for example 20 degrees, about the axis containing the atoms in the > benzene ring where the which are bonded to the -CH2- groups. > > Currently, I am trying to do this by attempting to create a plane containing > the aforementioned two atoms which would make an angle of 10 degrees with the > benzene ring and then I could REFLECT the NAMED SELECTION of the benzene ring > and the attached groups through this plane. However I don't know how to create > such a plane. The proper procedure is as follows: 1. Select the two atoms that define the axis you wish to rotate about. 2. Name the selection as LINE, using Select/Name Selection. 3. Select the structure that you wish to rotate about that axis. HyperChem will not allow one to rotate only part of a structure because of the danger of causing serious distortions of the bonds between the selected and unselected parts. Therefore: 4. Delete the bonds that join the selected part to the rest of the structure. Be careful to delete the bonds and not the atoms -- as necessary, use zooming (or the key) to let you right-click on the bond without touching an atom with the cursor. 5. Use Edit/Rotate; specify "Rotate About LINE", the angle, and that the rotation should Apply To Molecules. 6. Recreate the bonds that you had to break. Since you've been rotating about the axis defined by two of the atoms that define those bonds, those atoms will not have moved; the recreated bonds will be the same as the ones you broke. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Fri May 12 13:48:25 1995 Date: Fri, 12 May 1995 14:48:36 +0200 From: Matthias Glaser To: hyperchem@hyper.com Subject: modelling of complexes Hi netters, I'am new in this group and interested in modelling of technetium and rhenium complexes. Is there anybody who is also concerned with this or related topics? Please contact me. Thank you Matthias Glaser glaser@fz-rossendorf.de ________________________________________________________________________ From owner-hyperchem@hyper.com Fri May 19 13:26:45 1995 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: imcvey@Phoenix.kent.edu (McVey Iain) Date: Fri, 19 May 1995 10:26:48 +0100 Subject: Re: redox potentials via HOMO/LUMO? Cc: hyperchem@hyper.com > From: imcvey@Phoenix.kent.edu (McVey Iain ) > Subject: redox potentials via HOMO/LUMO? > To: hyperchem@hyper.com > Date: Thu, 18 May 1995 13:00:46 -0400 (EDT) > Greetings Hyperchemists, > > I am about to try to generate a corelation > between the HOMO and/or LUMO energies and the redox > potentials for a selection of organic molecules,the > selection of molecules I think I want to study are > likely to be quite heterogeneous (i.e. some aromatics, > aliphatics, olefins etc..) > > My question is: has this been done before, and > will it be necessary to use CI to obtain useful values > for the HOMO/LUMO energies? > > All suggestions warmly welcomed > > Iain McVey > > Graduate Student > Department of Chemistry > Kent State University > Kent, Ohio 44242 > > imcvey@phoenix.kent.edu > Dear McVey Iain! the correlations you attempt to establish have certainly been investigated for many years. For example, it is well known that polarographic half-wave reduction potentials for aromatic hydrocarbons correlate well with Huckel LUMO-energies (Streitwieser, "Molecular Orbital Theory for Organic Chemists", Wiley, 1961). It has little sense to include CI in a calculation MO energies. For an ordinary closed-shell molecule, consideration of interaction with singly excited configurations does not affect the SCF ground state (Brillouin's Theorem). If you include doubly or multiply excited configurations, you introduce electronic correlation effects and the ground state is stabilized, but the orbital concept "breaks down". Yours Sincerely, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark Internet: JSL@mmf.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ________________________________________________________________________ From owner-hyperchem@hyper.com Fri May 19 15:09:11 1995 Date: Fri, 19 May 1995 11:22:00 -0400 Content-Identifier: redox potentials From: Matthew.Harbowy@tjlus.sprint.com To: hyperchem@hyper.com Subject: redox potentials from MO work Part of my own interest in computation of redox potentials using Hyperchem is in determination of antioxidant activity. For a class of similar antioxidants, I tend to get good correlation between antioxidant activity and heat of reaction for one-electron oxidantion of antioxidant, but the correlation breaks down when comparing different classes of antioxidant. I consider this to be a limitation of a gas-phase model, where the change in 'molecular environment' for similar antioxidants should be about the same and thus cancel, but for widely different antioxidants, the effect of solution stabilization, polarization, etc., is different and produces a different effect. I have attempted to correlate excitation energies with antioxidant activity to no avail. I would imagine that the environment to which the electron is being transferred might affect the redox potential, since redox is always measured experimentally in reference to a particular 'electrode' and ionization is measured computationally with the electron going off into 'nothingness'. matt harbowy who can't speak authoritatively on redox to save his soul, nor is elucidating the views of thomas j. lipton, inc. ________________________________________________________________________ From owner-hyperchem@hyper.com Tue May 23 17:40:02 1995 Date: Tue, 23 May 1995 13:17:47 -0500 To: hyperchem@hyper.com From: paul@cellbio.wustl.edu (Paul H. Schlesinger) Subject: membrane proteins I would appreciate advice, comments, clever tricks from persons who have used hyperchem to model membrane proteins and membrane spanning peptides. How could one identify the membrane spanning domains to hyperchem? Can one have hyperchem place them into a "membrane" or segregate these portions of the protein structure appropiately. paul ________________________________________________________________________ From owner-hyperchem@hyper.com Wed May 24 18:50:23 1995 Date: Wed, 24 May 95 14:44:17 -0400 From: polowin (Joel Polowin) To: paul@cellbio.wustl.edu (Paul H. Schlesinger) Subject: Re: membrane proteins Cc: hyperchem@www > Date: Tue, 23 May 1995 13:17:47 -0500 > From: paul@cellbio.wustl.edu (Paul H. Schlesinger) > Subject: membrane proteins > > I would appreciate advice, comments, clever tricks from persons who have > used hyperchem to model membrane proteins and membrane spanning peptides. > How could one identify the membrane spanning domains to hyperchem? Can one > have hyperchem place them into a "membrane" or segregate these portions of > the protein structure appropiately. No membrane specialists here... though you should be able to set up a model "membrane" across a periodic box which would then simulate a larger sheet structure. You would set up a group of lipids, or whatever, in about the right structure, optionally with other molecules imbedded in the sheet. The chief problem with this is that the boundary conditions are periodic in three dimensions. If one tried to model a monolayer in a periodic box, molecules would migrate from the water side, across the boundary to the other side of the monolayer. I can see a couple of possible approaches to this problem. The simplest would be to model a bilayer instead of a monolayer; then having the same molecules on both sides of the lipid layer wouldn't be a problem. It should also be possible to create a sort of rigid barrier across one side of the box, by applying a lot of restrained-distance functions to a layer of molecules. This would be like having a layer of a molecular solid, covered with a layer of water (for example), topped by the monolayer. One could also perhaps use a layer of a structure such as graphite beneath the water molecules to prevent their migrating to the other side of the box. With these simulated barriers, it would be necessary to use a box sufficiently large that the "membrane" would be a long way from the "echo" of the back side of the barrier. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Thu May 25 05:24:38 1995 Date: Wed, 24 May 1995 23:49:18 -0700 From: chrisluc@ix.netcom.com (Chris Lucier) Subject: Organic reactions? To: hyperchem@hyper.com I'm relatively new to hyperchem. Does any one know if it is possible to "run" reactions ie claisen condensations,haloform reactions, etc. and if it is how would you go about doing it. Thanks Chris Lucier chrisluc@ix.netcom.com glamdrig@u.washington.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Thu May 25 15:18:46 1995 Date: Thu, 25 May 95 10:59:59 -0400 From: polowin (Joel Polowin) To: chrisluc@ix.netcom.com (Chris Lucier) Subject: Re: Organic reactions? Cc: hyperchem@www > Date: Wed, 24 May 1995 23:49:18 -0700 > From: chrisluc@ix.netcom.com (Chris Lucier) > Subject: Organic reactions? > > I'm relatively new to hyperchem. Does any one know if it is possible to > "run" reactions ie claisen condensations,haloform reactions, etc. and > if it is how would you go about doing it. I should point out that although one can model reactions with HyperChem, it is not particularly well suited to modelling reactions in bulk, in an attempt to determine optimal reaction conditions, side reactions, alternate products, etc. But you can, for example, run semi-empirical molecular dynamics calculations on two organic units such that they collide and react, giving products that separate from the site of reaction. By using the 'snapshot' option, the coordinates of the atoms are saved periodically during the simulation; then you can retrieve the configuration of the system at any point, including the period when the system is rearranging. The system could also be set up with a reasonable set of internal vibrations and rotations at the beginning of the simulation to give an appropriately complex model. In order to model a bulk reaction, you would have to repeat the simulation many times, choosing the initial orientations and positions and motions of the reacting species from the appropriate statistical distributions. I can send a more detailed description, and a sample .HIN file or two, to anyone who's interested. The information is also available on our WWW page under "Support / Frequently asked questions / How can I simulate a reaction?" Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem Mon May 29 09:32:54 1995 Return-Path: doyne@rs6chem.vill.edu Date: Mon, 29 May 1995 09:32:44 -0400 To: hyperchem@hyper.com From: doyne@rs6chem.vill.edu (Thomas H. Doyne) Subject: E-mail address change Please be advised that effective 25 May 1995, my E-mail address has been changed from doyne@ucis.vill.edu to doyne@rs6chem.vill.edu Thank you, Thos. H. Doyne