From chemistry-request@ccl.net Sun Sep 21 20:00:01 2003 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8LNxTmK000429 for ; Sun, 21 Sep 2003 19:59:29 -0400 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id 9AA56483D for ; Sun, 21 Sep 2003 19:34:00 -0400 (EDT) Received: from 200.165.141.50 (SquirrelMail authenticated user gustavo) by mercury.chem.pitt.edu with HTTP; Sun, 21 Sep 2003 19:34:00 -0400 (EDT) Message-ID: <1049.200.165.141.50.1064187240.squirrel(at)mercury.chem.pitt.edu> Date: Sun, 21 Sep 2003 19:34:00 -0400 (EDT) Subject: CCL:INDO/S with double excitations - SUMMARY From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL readers, here you have the answers I received for my question about including double excitations in a INDO/S CI. I Thank Deepak Singh and Shahar Keinan for answering my question. Sincerely yours, Gustavo L.C. Moura gustavo(at)mercury.chem.pitt.edu --------------------------------------------------------------- Original question: Dear CCL readers, I have been reading papers dealing with the Sum Over States (SOS) calculation of two-photon absorption cross sections of organic molecules with the INDO/S methodology. In these papers the authors include single and double excitations in the CI. As far as I know, the INDO/S methodology was parameterized for single excitations only. The authors of these papers don't say why they need to include double excitations in the calculations. Does someone on this list know the reason for including these double excitations in these INDO/S calculations? Thank you very much in advance. I will summarize. Sincerely yours, Gustavo L.C. Moura gustavo(at)mercury.chem.pitt.edu Answer #1: Dear Gustavo, The INDO/S was parameterized for single excitation (actually, for a window of CIS 10 10), but the double excitations can be used, with caution. You have to make sure, by comparing to experimental known data, what is better to use. An example can be found at: Optical limiting chromophores. Correlation effects in computing triplet-triplet absorption energies of organic molecules Albert IDL, Marks TJ, Ratner MA, Rauh RD JOURNAL OF PHYSICAL CHEMISTRY A 104 (4): 837-844 FEB 3 2000 Also, if you're using the old ZINDO code, there are some known problems with using larger window of excitation than CIS 10 10 and CID 5 5 - mainly memory allocations, so make sure that you code does this without writing on data and getting gibberish. Hope it helps, Shahar Answer #2: Gustavo, It has been some time since I worked in this area, but for many systems, e.g. polyenes, it is necessary to include double CI, as the low-lying energy state are forbidden for one-photon transitions. To get a more accurate representation of the energy states, it is essential to use single and double CI. Please look at the MNDO-PSDCI methods which my former research group has used to study polyene, and retinal-like molecules Stuart, J. A., B. W. Vought, C. F. Zhang, and R. R. Birge. 1995. The active site of bacteriorhodopsin. Two-photon spectroscopic evidence for a positively charged chromophore binding site mediated by calcium. Biospectroscopy. 1:9-28. Martin, C. H., and R. R. Birge. 1998. Reparameterizing MNDO for excited state calculations using ab initio effective Hamiltonian theory: application to the 2,4-pentadien-1-iminium cation. J. Phys. Chem. A. 102:852-860. Sincerely, -- Deepak ------------------------------------------------------------------------------- Deepak Singh, Ph.D. Product Specialist, Simulations Accelrys 9685 Scranton Road San Diego, CA 92121-3752 Tel: 858-799-5207 Cell: 858-449-8790 Email: dsingh(at)accelrys.com ------------------------------------------------------------------------------- From chemistry-request@ccl.net Sun Sep 21 10:33:41 2003 Received: from mail1.cc.huji.ac.il (mail1.cc.huji.ac.il [132.64.1.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8LEX9mK013598 for ; Sun, 21 Sep 2003 10:33:09 -0400 Received: from localhost.localdomain (localhost.localdomain [127.0.0.1]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id 6D5EA400EC; Sun, 21 Sep 2003 17:32:58 +0300 (IDT) Received: from mail1.cc.huji.ac.il (localhost.localdomain [127.0.0.1]) by localhost.localdomain (VaMailArmor-2.0.1.14) id 08941-3AF5BCDD; Sun, 21 Sep 2003 17:32:58 +0300 Received: by mail1.cc.huji.ac.il (Postfix, from userid 31998) id 11C66400EC; Sun, 21 Sep 2003 17:32:36 +0300 (IDT) Received: from md.huji.ac.il (md.huji.ac.il [132.64.169.2]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id BEADD40089 for ; Sun, 21 Sep 2003 17:32:35 +0300 (IDT) Received: from amiram12.md.huji.ac.il (amiram12.md.huji.ac.il [132.64.165.247]) by md.huji.ac.il (8.12.9/8.12.9) with ESMTP id h8LEWauO466400 for ; Sun, 21 Sep 2003 17:32:36 +0300 (IDT) Content-Type: text/plain; charset="iso-8859-1" From: Tal Lavy Subject: CCL:Software for generating conformations Date: Sun, 21 Sep 2003 17:33:05 +0300 User-Agent: KMail/1.4.3 To: CHEMISTRY..at..ccl.net MIME-Version: 1.0 Message-Id: <200309211733.05639.tallavy..at..md.huji.ac.il> X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_KMAIL version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.14; VAE: 6.21.0.1; VDF: 6.21.0.49; host: mail1.cc.huji.ac.il) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8LEXgmK013621 Dear All, I am looking for a free program that could generate (and output) conformations of molecules, according to specifications of rotations around bonds, by the user. This means the user constructs the molecule and the program reads it in PDB format, then the user inputs a set of angles (30, 65, 115, 40, 150 etc..) and the program outputs the transformed coordinates for the structure. These structures should then undergo a force field evaluation. Thank you very much, Tal =========================================================== Tal Lavy, Molecular Modeling and Drug Design Department of Medicinal Chemistry and Natural Products School of Pharmacy Hebrew University of Jerusalem ISRAEL Phone: 972-2-6757026 Fax: 972-2-6758925 e-mail: tallavy..at..md.huji.ac.il http://www.md.huji.ac.il/models ============================================================