From owner-chemistry@ccl.net Thu Apr 19 08:45:01 2007 From: "Henry N. Pangamte hpangamte- -yahoo.com" To: CCL Subject: CCL:G: Keyword for biradical in Gaussian 03 Message-Id: <-34072-070419005901-31115-IX+YKBGHv7Wf/+0/C13s6g!=!server.ccl.net> X-Original-From: "Henry N. Pangamte" Date: Thu, 19 Apr 2007 00:58:57 -0400 Sent to CCL by: "Henry N. Pangamte" [hpangamte .. yahoo.com] Dear CCLers, I am running quantum calculations on benzyne systems using DFT methods. For geometry optimisation,do we need to write the keyword biradical in the method section in Gaussian 2003?currently i am using b3lyp/6-31g**.Please give me more indept information for singlet biradical geometry optimisation in Gaussian 2003.Thanks. Henry N.pangamte NEHU,Shillong Megahlaya,India hpangamte() yahoo.com From owner-chemistry@ccl.net Thu Apr 19 11:43:01 2007 From: "Jed Zaretzki zaretj .. rpi.edu" To: CCL Subject: CCL: Going from a Topology File to a .top File for an AMBER Forcefield Message-Id: <-34073-070419110049-4150-UGWA7olcgIvsdBin7CwE4Q**server.ccl.net> X-Original-From: "Jed Zaretzki" Date: Thu, 19 Apr 2007 11:00:45 -0400 Sent to CCL by: "Jed Zaretzki" [zaretj++rpi.edu] Hi all, I am looking for a tool which will go from a bare bones .pdb file to a .top file. .pdb file should be considered a topology file. .top file can be considered a detailed topology file with additional force field information required to calculate partial charges upon the individual atoms of the molecule (those partial charges are also in the file). I need this tool to work for small molecules with at most 60 or 70 heavy atoms. I also need it to work with an AMBER forcefield. Initial Information in .pdb (or equivalent) file: Atom Type - no special types, equivalent to the atomic weight. XYZ atomic coordinates Bond Connectivity information, inluding whether they are single, double or triple bonds. Final Information in .top (or equivalent) file. Atom Type - Specifically AMBER type with unique sigma and epsilon values. XYZ atomic coordinates. Bond Connectivity, including strength, defined by Leonard Jones Potential of AMBER atom types. Atom Partial Charges according to Amber Forcefield. All valid angles. All valid dihedral angles (torsions). Thanks a lot, Jed From owner-chemistry@ccl.net Thu Apr 19 14:11:01 2007 From: "Robert W. Zoellner rwz7001-,-humboldt.edu" To: CCL Subject: CCL: Plastic candy bar wrappers Message-Id: <-34074-070419135903-11472-fV4R8CxEwlVrfle3iJseDw||server.ccl.net> X-Original-From: "Robert W. Zoellner" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 19 Apr 2007 10:58:46 -0700 Mime-Version: 1.0 Sent to CCL by: "Robert W. Zoellner" [rwz7001-*-humboldt.edu] Greetings All! So, I was fortifying myself for the remainder of the morning with a cup of tea and a candy bar (nothing but the best in nutrition!) and came upon this observation: When I attempted to tear open the candy bar wrapper from one end at the point where the two sides of the wrapper were sealed together by holding on to the overlapped sides and tearing, I could not get the plastic to begin to tear. However, when I did the same thing at the other end of the candy bar wrapper, the plastic tore easily. Does anyone with some knowledge of polymers know why I could tear the plastic from one end and not from the other? (There were little regular jagged edges at each end -- as if the plastic were cut with a pinking shears as would be done with cloth.) This is obviously not of great import, but I was hoping that someone would have an answer. All the best, Bob Z. Robert W. Zoellner, Ph.D. Professor and Chair Department of Chemistry Humboldt State University One Harpst Street Arcata, California 95521-8299 telephone: (707) 826-3244 fax: (707) 826-3279 From owner-chemistry@ccl.net Thu Apr 19 15:53:01 2007 From: "Xu Lv olangtea,+,yahoo.com" To: CCL Subject: CCL: How to do CIS opt and excited state calculations? Message-Id: <-34075-070419115821-15250-4UdI9v1MfI3K0+knb0yOeg|,|server.ccl.net> X-Original-From: "Xu Lv" Date: Thu, 19 Apr 2007 11:58:18 -0400 Sent to CCL by: "Xu Lv" [olangtea%a%yahoo.com] Dear members, I have basic doubt in CIS calculation. I know how to do tddft calculation but no experience in CIS. Is it just like tddft? Can you tell me the following procedure is correct? (1) optimization of the first excited state geometry CIS(Root=1)/6-31g* opt SCRF(pcm, solvent=water) (2)CIS-excited state calculation using CIS-first excited state optimized geometry CIS(Nstates=10, Singlets)/6-31g* SCRF(pcm, solvent=water) In the step (1), it will optimize the geometry of only the first excited state. Is it good to use the first excited state optimized geometry to study the S0 to S2 or S3 etc. transition (as the step (2) will calculate 10 states)? Please give me your useful comments. Thank you very much. From owner-chemistry@ccl.net Thu Apr 19 21:16:00 2007 From: "Vedbar Singh khadka vedbar _ gmail.com" To: CCL Subject: CCL:G: Problem regarding using of Gaussian 03W Message-Id: <-34076-070419191424-21192-oab1k5oxj7QLCPJxQvmK3A(-)server.ccl.net> X-Original-From: "Vedbar Singh khadka" Date: Thu, 19 Apr 2007 19:14:21 -0400 Sent to CCL by: "Vedbar Singh khadka" [vedbar%%gmail.com] By knowing the imaginary part of the second hyperpolarizability (; , ,- ), we can calculate the two photons absorption cross-section ()of a molecule in Gaussian 03 software. Please suggest me the procedure to calculate second hyperpolarizability and use it to obtain the two-photon absorption cross-section using the Gaussian 03W software. From owner-chemistry@ccl.net Thu Apr 19 23:07:01 2007 From: "Thomas Joseph alabarae . yahoo.com" To: CCL Subject: CCL: is there any hydrophobic group comparable with Bromine atom Message-Id: <-34077-070419230327-27284-8P6nObCXv/bTxqoOoS+H7g||server.ccl.net> X-Original-From: "Thomas Joseph" Date: Thu, 19 Apr 2007 23:03:23 -0400 Sent to CCL by: "Thomas Joseph" [alabarae]-[yahoo.com] is there any hydrophobic group comparable with Bromine atom. Is there any website, which gives you the details and order of hydrophilic and hydrophobic atoms/groups From owner-chemistry@ccl.net Thu Apr 19 23:41:01 2007 From: "Richard Huhn huhnra^^mit.edu" To: CCL Subject: CCL:G: Basis sets for ONIOM in G03 Message-Id: <-34078-070419232756-3433-h65nYlogQQrtNsJG9qauQg|*|server.ccl.net> X-Original-From: "Richard Huhn" Date: Thu, 19 Apr 2007 23:27:52 -0400 Sent to CCL by: "Richard Huhn" [huhnra-$-mit.edu] I am using Gaussian 03 to do ONIOM calculations of some very large molecules containing transition metals. I have a two-part question: Is it possible to use two DFT methods in an ONIOM calculation? For example, the high level could use a different functional than the lower level(s); or, the high level could use a larger basis set than the lower level(s). If either of these cases are possible, how does one input a general basis set (as with the GenECP keyword) that will supply the different basis sets for the different levels? This problem is not encountered in the examples in the G03 manual, in which only MM or semi-empirical methods are used as the low layer. An example of a working input file would be greatly helpful. Thank you for any help or pointers! Rich Huhn