From mallon@rzmain.rz.uni-ulm.de Wed Sep 23 13:38:02 1992 Date: Wed, 23 Sep 92 11:38:02 +0200 From: mallon@rzmain.rz.uni-ulm.de To: "CHEMISTRY@ccl.net"@netway.rz.uni-ulm.de Subject: Problem with bond-interactions in PCILO Hello ! In my diploma work I am dealing with methods of Molecular Modeling. The method I use is a semi - empirical quantummechanical one named PCILO (Perturbative Configuration Interaction Using Localized Orbitals). To make it easy to understand how this method works let me first explain it going through the initials of the abbreveation. LO : means we are dealing with localized orbitals. How do we get them ? We know the s and p orbitals we obtain from analysing H - problem. Lets call the s and p orbitals atomic orbitals (AO). To get a description of the bond between two atoms we assume there are only two hybrid-orbitals (HO) making up the bond, one belonging to each atom involved. These HOs are made up of AOs. (sp, sp2, sp3). At this point we are able to give a description of our molecule in a non excited state, just by buiding a Hartree-Product with all our obtained descriptions of the bonds (we will call a bonding orbital a molecular oribtal furtheron). First we assume that no bond is in an excited state, so we got something like a ground state of the molecule. Then we allow simply and doubly excited configurations, meaning that one or two electrons switch to an excited state. (This switching does not necesserily mean that the electron stays with the bond it originated from. It may leave and *travel* into another orbital where it will have to occupy an excicted level due to the fact that the non- excited levels are and stay occupied). So this gives us some more "allowed" configurations for example there are now n single excited configurations, n being the number of the bonds in our molecule. And there are n(n-1)/2 doubly excited configurations. CI : We will now proceed and do a description of our molecule using the configurations produced above. This we do by using a configuration interaction (CI) method. We add those configurations and weigh them with a factor. Our next problem is how to get the weighing coefficients. P : Assuming that the nonexcited configuration is real close to the result, we are doing a non-time-dependent perturbation expansion (Raleigh-Schroedinger-perturbation-expansion). Due to some trick (which I am not going to explain in detail, Keywords are Moller-Plesset, Epstein-Nesbet) the results of the perturbation expanison may be interpreted physically. We obtain a resulting term for our systems wavefunction and energy each. Special about these terms are the following facts : - the term of first order Psi(1) and E(1) did vanish due to the above mentioned trick, a special decomposition of our Hamiltonian. - The terms of second order Psi(2) and E(2) now reflect an interaction of those excited configurations with the groundstate configuration. This allows to say which interaction of which bonds gives what addition to the systems total energy. Let us now take a look at those excited configurations again. 1. simply excited configurations There are two ways of getting a simply excited configuration : a. the electron gets excited, but stays with the bond it originated from. This leads to a polarisation of the bond. b. The electron gets excited and *decides* :-) to go and travel around. This is a charge delocation effect. If the electron stays in the molecule it originated from we call this charge shift, if it heads forward to another molecule this will be called charge transfer. 2. doubly excited configurations Like in 1. there are several cases to discuss. But I am only intersted in the following : Two bonds are loosing electrons to the excited state, but both electrons stay with their originating bonds. Now those excited orbitals are doing an interaction which we call dispersion-interaction. Now the problem I am dealing with : Benzene (c6h6) is a molecule with a mesomeric structure. The HOs uses for describing the bonds are of type sp2. The pi - eletrons do form a delocalized electronic system. A part of my work is to do a visualization of the effects mentioned above. When I do the display of the strongest dispersion interactions in benzene I get some amazing results. My expectation (please note : classically thoughts now) would be that bonds being next neighbours (I am talking of the ring-system here) would interact the most. Next would then be the interactions between overnext partners. The results I get to see are exactly the opposite. Strongest are overnext bonds interactions, then I find the next neighbours interactions. My first thought was that the treatment of the mesomeric structure containes still some errors, but this was proved as wrong. Each c-c bond is treated as 1.5 times single bond and so are the interactions. Now I am thinking of some quantummechanical effect that could explain this. Perhaps somebody has an idea or a clue ? I would be glad to get some opinions from you. I am right now thinking about an effect caused by the spin of the electrons involved (-> Paulis principle etc.) But I havent reached a state of clear thought yet. Thanks for reading, RaMa. ----------------------------------------------------------------------- | Rainer "RaMa" Mallon | | | University of Ulm, Germany | I am an instant swimmer ... | | Department of Applied Physics | ... just add water ! | | mallon@main01.rz.uni-ulm.de | | ----------------------------------------------------------------------- From mckelvey@Kodak.COM Wed Sep 23 03:31:40 1992 Date: Wed, 23 Sep 92 07:31:40 -0400 From: mckelvey@Kodak.COM To: osc@Kodak.COM Subject: MP2 disk requirements Could someone give me an estimate, or suggest how to do the estimate myself, for the amount of scratch space required for an MP2/6-31g* geometry optimisation on styrene ? (C8H8,28 occupied mo's, 138 ao's) I am using G90 on RS6000. Any suggestions about the optimum way to go about such a calculation of this size would be welcomed. I would guess this will take 3-5 days of cpu time. Many thanks in advance, and I will pass the comments back. John McKelvey Res. Labs Eastman Kodak Co. Rochester, NY 14650-2216 MCKELVEY@KODAK.COM 716-477-3335 From richard@TC.Cornell.EDU Wed Sep 23 10:02:19 1992 Date: Wed, 23 Sep 1992 14:02:19 -0400 From: Richard Gillilan To: chemistry@ccl.net Subject: FAQ: description of pdb format Hi, does anyone know where I can find a description of the brookhaven pdb file format? Thanks Richard Gillilan Visualization Specialist Cornell Theory Center From ravishan@swan.wesleyan.edu Wed Sep 23 16:54:44 1992 Date: Wed, 23 Sep 92 20:54:44 -0400 From: G. Ravishanker To: chemistry@ccl.net Subject: Molecular Modeling Folks I am preparing to give a talk on Molecular modeling hardware and software. I have already collected information on major software and hardware platforms used in modeling, based on what I have seen presented in some of the meetings as well as based on what we use here at Wesleyan. I do not have much information on PC-based (386, 486 and Mac) modeling software except for Hyperchem. I am looking for information on any kind of modeling information, starting from small molecules to large biomolecular systems. If anyone can point me to some review article, or some kind of directory, it will be of great help. If you are a commercial vendor and want to send me some stuff, I will be more than happy to hear from you on what you have to offer. Thank you in advance. Ravi From jomal@chopin.dfq.ufrj.br Wed Sep 23 23:25:13 1992 Date: Wed, 23 Sep 1992 23:25:13 GMT From: jomal@chopin.dfq.ufrj.br (Joao Otavio M.A. Lins) To: chemistry@ccl.net Subject: PaintJet config question Hello net friends! I came to the list with a non-proper question regarding "how to configure my HP PaintJet XL using the virtual printer option under SMIT /AIX 3.2", but I'm looking forward for this information a lot of time with no answers, even from IBM. If you have any kind of information that will do my HP works, please send replies directly to me. Thanks in advance, Joao O.M.A. Lins Dept. Fisico-Quimica / IQ-UFRJ PHONE: (055)(021) 590-9890 FAX : (055)(021) 290-4746 EMAIL: jomal@chopin.dfq.ufrj.br jomal@ufrjvms1.bitnet