From chemistry-request@server.ccl.net Thu Aug 26 09:15:30 1999 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA04082 for ; Thu, 26 Aug 1999 09:15:30 -0400 Received: from gaigalas_b216 (h194129.nist.gov [129.6.194.129]) by email.nist.gov (8.9.3/8.9.3) with SMTP id JAA09645 for ; Thu, 26 Aug 1999 09:09:20 -0400 (EDT) Message-Id: <3.0.32.19990826085429.0098aa90@mailserver3.nist.gov> X-Sender: gaig@mailserver3.nist.gov X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 26 Aug 1999 08:54:29 -0400 To: chemistry@ccl.net From: Adolfas Gaigalas Subject: fluorescein vibrations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Are there calculations of the vibrational frequencies of fluorescein? Of special interest is the difference in the spectra between monoionic and diionic forms of fluorescein. Adolfas Gaigalas Biotechnology Division NIST (301)975 2873 adolfas.gaigalas@nist.gov From chemistry-request@server.ccl.net Thu Aug 26 09:41:36 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA04214 for ; Thu, 26 Aug 1999 09:41:36 -0400 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id JAA27778 for ; Thu, 26 Aug 1999 09:35:27 -0400 (EDT) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862567D9.004A2346 ; Thu, 26 Aug 1999 08:29:46 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: CHEMISTRY@www.ccl.net Message-ID: <862567D9.004A202C.00@unomail.unomaha.edu> Date: Thu, 26 Aug 1999 08:29:34 -0500 Subject: formate vs. allyl follow-up Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline As a follow-up to the previous post, if I run a HF/6-31G* calculation on the formate anion, the HOMO matches the Huckel HOMO and the LUMO macthes the Huckel LUMO. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Thu Aug 26 10:53:55 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04566 for ; Thu, 26 Aug 1999 10:53:55 -0400 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA02458 for ; Thu, 26 Aug 1999 10:47:39 -0400 (EDT) Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id QAA09029 for ; Thu, 26 Aug 1999 16:47:20 +0200 (MET DST) Received: from pc03.chemie.uni-jena.de by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA23671; Thu, 26 Aug 1999 16:47:20 +0200 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <37C55377.31D2@pc04.chemie.uni-jena.de> Date: Thu, 26 Aug 1999 16:47:19 +0200 From: Andreas Goeller X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: nbo4.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, can onyone tell me where to get NBO 4.0 (with natural resonance theory) to combine it with Gamess? -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Aug 26 12:16:48 1999 Received: from students.su.se (students.su.se [130.237.89.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05025 for ; Thu, 26 Aug 1999 12:16:47 -0400 Received: from falco (falco.biokemi.su.se [130.237.179.113]) by students.su.se (8.8.8/8.8.8) with SMTP id SAA09822 for ; Thu, 26 Aug 1999 18:10:41 +0200 (MET DST) Sender: fredrik@students.su.se Message-ID: <37C56779.167E@students.su.se> Date: Thu, 26 Aug 1999 18:12:41 +0200 From: Fredrik Tholander X-Mailer: Mozilla 3.04GoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: ccl/question/Autodock3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL users How is the pdbqs file used in Autodock3? It seems to me that it isn't directly needed in order to perform a docking simulation? I haven't found any detaied explanation about the pdbqs file in the Autodock documentation. My docking results have been fairly alright but not completely satisfactory. Please help, Fredrik Tholander, dep of Biochem, Stockhol University e-mail: m69ft55c@students.su.se From chemistry-request@server.ccl.net Thu Aug 26 09:13:52 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA04061 for ; Thu, 26 Aug 1999 09:13:52 -0400 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id JAA27216 for ; Thu, 26 Aug 1999 09:07:44 -0400 (EDT) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862567D9.00479898 ; Thu, 26 Aug 1999 08:02:01 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: CHEMISTRY@www.ccl.net Message-ID: <862567D9.0047956E.00@unomail.unomaha.edu> Date: Thu, 26 Aug 1999 08:01:50 -0500 Subject: Allyl pi system vs. format pi system Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CClers, I have question about molecular orbitals (MO) generated by simple Huckel calculations involving just conjugated p-orbitals and MO generated via semi-empirical calculations using all of the atomic valence orbitals. Specifically, the differences in calculating the allyl pi system vs. the formate (HCO2-) pi system. Both systems have 3 p orbitals that combine to form the familiar Huckel orbitals, we'll call them HMO1, HMO2, and HMO3. Since the allyl cation system has just two electrons, HMO1 is the HOMO and HMO2 is the LUMO. If one does a semi-empirical calculation using all valence obitals on the allyl cation system (AM1 or PM3), a graphical representation of the HOMO matches the familiar all bonded HMO1 and the LUMO matches the HMO2. However, with the formate system, a semi-empirical calculation does not produce a HOMO the matches HMO2 (with four electrons in this pi system, HMO2 is the HOMO). The HOMO generated by the semi-empirical method not only has significant coefficients on both oxygens, but also has a large coefficients on the hydrogen (connected to the middle carbon). The HMO2 for formate matches HOMO-1 in the semi-empirical calculation not HOMO. The question is, why does the semi-empirical method for formate generate a HOMO that is different than that predicted by simple Huckel theory? I understand the latter has only 3 atomic orbitals as a basis set while the former has 13 by including all valence orbitals. Can this change the order of MO we are accustom to when we think of Huckel explanations of electron delocalization? Why would the allyl cation system match semi-empirical but not the formate, is symmetry involved? Thanks in advance for any insight. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Thu Aug 26 10:03:13 1999 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04343 for ; Thu, 26 Aug 1999 10:03:12 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id PAA25116 for ; Thu, 26 Aug 1999 15:59:56 +0200 (MET DST) Date: Thu, 26 Aug 1999 15:59:56 +0200 (MET DST) Message-Id: <199908261359.PAA25116@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Summary: RPA and second quantization Hi CCL'ers I want to thank the many responses I received to my question: I'm currently studying polarization propagator techniques like RPA and MBGF. Does anyone know to what the following names are related to: Random Phase and Second Quantization. I know more or less what it is about, but I don't seem to find the connection between the theory and the name it is given to. -- 1 -- Dear Sergiusz: Try D. Pines and P. Nozieres beautiful book, The Theory of Quantum Liquids (W. A. Benjamin, Menlo Park, CA, 1966). Also Bohm's book on quantum mechanics has a nice treatment of second quantization (don't recall the exact title, but I can get it for you if you can't find it). - Susan _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ Susan R. Atlas _/ _/ Department of Physics and Astronomy _/ _/ The University of New Mexico _/ _/ 800 Yale NE email: susie@sapphire.phys.unm.edu _/ _/ Albuquerque, NM 87131 Phone: (505) 277-1509 _/ _/ _/ _/ http://www.phys.unm.edu/CompMaterials _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ -- 2 -- These concepts have originated in physics. Second quantization deals with the algebra of creation and annihilation operators and connects quantum field theory with many-body theories. A simple introduction to second quantization is given in Szabo and Ostlund: Modern Quantum Chemistry (Dover 1996). More can be found out from books on quantum mechanics (for instance, Baym's Lectures on quantum mechanics). The random phase approximation (RPA) is, what I can see, not treated in Szabo's and Ostlund's book, although it gives a good introduction to Green's functions. RPA is an approximation to the two-body Green's function, and was first used by in a paper by Bohm and Pines (Phys. Rev. 92, 609 (1953)) to describe plasma oscillations by assuming random phases. RPA is decribed in books on many-body theories, for instance G.E. Brown: Many-body problems, North-Holland, 1972 (probably there are some books on quantum chemistry that have it, too). Greetings, TS Tom Sundius University of Helsinki, Department of Physics phone +358-9-191 8339 P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 -- 3 -- My favorite source is Blazot and Ripka's "Quantum theory of finite systems". This has a pretty comprehensive overview of RPA methods, second quantization, etc. and (more importantly) what physical process is being represented. I'm not exactly sure of the origins of the "name" RPA. However, I'm pretty sure it's connected to the fact that in RPA, one assumes that the excitations are collective and bosonic in form. In other words, the basic RPA assumption is that the excitation operators, A and A^+, are the operators a boson (i.e harmionic oscillator) algebra, [A,A^+] \approx 1 and hence generate coherent state excitations from the RPA vacuum defined as A|0> = 0. The A's themselves are related to elementary particle/hole excitations and de-excitations via a cannonical Bogliobov transformation. Again, most of this is in Blazot and Ripka. If you're interested in a 2nd quantization derivation of all this, check out one of my recent papers: Car-Parrinello molecular dynamics on excited state surfaces. E. R. Bittner and D. S. Kosov, J. Chem. Phys. 110, 6645 (1999) To save your self a trip to the library, here's a link to the PDF version of the paper: http://k2.chem.uh.edu/bittner/Papers/CPMD.pdf -Cheers! ERB -- Eric R Bittner, Asst. Professor ph: 713-743-2775 Dept. of Chemistry fax:713-743-2709 University of Houston, Houston TX 77204 email: bittner@uh.edu "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein -- 4 -- I recommend that you have a read of the following book, "second quantization-based methods in quantum chemistry" by Poul Jorgensen and Jack Simons (Academic Press , New York,1981) Its pretty extensive and describes the RPA ( also known as Time-dependant Hartree-Fock TDHF) in terms of second quantization. As a very simple explanation I would say that first-quantization is the consideration of particles (electrons etc) as wavefunctions , and theory based on waves is thus in a first-quantized method. Second quantization essentailly converts wave ideas back to a particle description, thus one constructs wavefunctions from operators that either create or annihilate a particle from a given state. noj _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Thu Aug 26 11:13:24 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04687 for ; Thu, 26 Aug 1999 11:13:22 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@server.ccl.net; Thu, 26 Aug 1999 17:07:13 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id RAA16000; Thu, 26 Aug 1999 17:07:12 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37C5581F.24BB2F9@physik.tu-muenchen.de> Date: Thu, 26 Aug 1999 17:07:12 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: mehmacc presentation with opendx Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether, Can anybody send me one or some more of his example files (.net files) produced with the opendx4.0(6) explorer which are representations of mehmacc files especially from .elf or .rho files. All my own representations are very strange. In this regard my second question how can I produce representations of the electron localization function of one molecule together respective without the nucleus frame? Thanks in advance Th. Mehnert From chemistry-request@server.ccl.net Thu Aug 26 14:56:57 1999 Received: from scrabble.freeuk.net (scrabble.freeuk.net [212.126.144.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05894 for ; Thu, 26 Aug 1999 14:56:52 -0400 Received: from [212.126.150.209] (helo=compaq) by scrabble.freeuk.net with esmtp (Exim 2.11 #1) id 11K4bd-00013w-00 for chemistry@ccl.net; Thu, 26 Aug 1999 18:50:37 +0000 Message-Id: <4.2.0.58.19990826194611.03a30950@icex5.cc.ic.ac.uk> X-Sender: ic\seth\s.hogg@icex5.cc.ic.ac.uk X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 26 Aug 1999 19:47:46 +0100 To: chemistry@ccl.net From: Simon Hogg Subject: GAMESS vs. GAMESS-UK ? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Does anyone know of a resource giving a comparison of GAMESS and GAMESS-UK? I can't find anything on altavista. I;m not really interested in benchmarks, but more capabilities. -- Simon Hogg